DE CANARY G vs P - gender corrected
Mafe Senosain
5/6/2020
Pre-processing of the data
ls_preprocessed <- preprocess_rna(path_rnaseq = 'rnaseq.RData', correct_batch = T, correct_gender = T)Exploring data
Batch effect correction
print(ls_preprocessed$pbatch_bf)
print(ls_preprocessed$pgender_bf)
print(ls_preprocessed$pbatch_af)
print(ls_preprocessed$pgender_af)
DE analysis
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=FALSE,
pDataBased=TRUE,
NewCondition=FALSE,
cond_nm='CANARY',
two_levels=c('P','G'),
reference = 'G',
correct_gender=TRUE)## Unlist done## Labeling done## Filtering done## factor levels were dropped which had no samples## Design done## factor levels were dropped which had no samples## Warning: Column `gene`/`ENSEMBL` joining character vector and factor, coercing
## into character vector## Warning: Setting row names on a tibble is deprecated.## vsd symbols done## using pre-existing size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 2330 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## DESeq done## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895## Warning: Column `gene`/`ENSEMBL` joining character vector and factor, coercing
## into character vector## res symbols done## list doneDE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)
volcano_plot(DE_res$res_df, gene=NULL, p_title='CANARY: G vs P')
pCutoff=0.05
FCcutoff=1.5
x <- DE_res$res_df %>%
filter(., abs(DE_res$res_df$log2FoldChange) >FCcutoff &
DE_res$res_df$padj < pCutoff)
x## baseMean log2FoldChange lfcSE stat pvalue padj
## 1 100.963946 -1.848747 0.4892309 -3.915950 9.004881e-05 4.598978e-02
## 2 43.570278 -2.093049 0.4853680 -3.946672 7.924501e-05 4.403648e-02
## 3 2662.931461 -2.188810 0.3978778 -5.451827 4.985501e-08 4.328536e-04
## 4 237.682033 -2.572291 0.4074854 -6.202286 5.564881e-10 1.932628e-05
## 5 382.807966 1.724855 0.4858152 3.987806 6.668728e-05 4.158190e-02
## 6 433.120858 -2.881735 0.4910630 -5.035885 4.756466e-07 2.753122e-03
## 7 120.052178 1.521712 0.4927704 4.157896 3.211918e-05 2.535153e-02
## 8 1527.378751 2.107586 0.4828562 5.702435 1.181081e-08 2.050888e-04
## 9 12.222654 -2.111182 0.4900170 -3.970904 7.160034e-05 4.214590e-02
## 10 712.442304 1.613042 0.3948269 4.223690 2.403342e-05 2.384733e-02
## 11 236.094383 -1.563003 0.3612279 -4.298532 1.719330e-05 2.074459e-02
## 12 191.555276 1.723043 0.4595120 4.162036 3.154221e-05 2.535153e-02
## 13 7.065478 -2.030874 0.4068022 -4.275961 1.903147e-05 2.203146e-02
## 14 398.390516 1.553835 0.3971247 3.984595 6.759538e-05 4.158190e-02
## 15 6.860489 -2.611171 0.4932345 -4.307902 1.648105e-05 2.074459e-02
## 16 5.460123 -1.902140 0.4287445 -4.532341 5.833360e-06 1.191687e-02
## 17 42.356684 -1.861706 0.4446733 -3.982314 6.824753e-05 4.158190e-02
## 18 59.646887 -1.879359 0.3957899 -4.667905 3.042860e-06 8.806291e-03
## 19 1623.855258 -2.065864 0.4473549 -4.257487 2.067381e-05 2.316067e-02
## 20 113.114649 1.583771 0.4575157 3.973403 7.085307e-05 4.214590e-02
## 21 250.271673 -1.749145 0.4146469 -4.130964 3.612445e-05 2.727317e-02
## 22 496.594867 -2.340439 0.4919902 -4.588341 4.467828e-06 1.034421e-02
## 23 16.553277 -2.570156 0.4531783 -5.463635 4.664829e-08 4.328536e-04
## 24 32.060340 -2.431115 0.4833518 -4.940304 7.800069e-07 3.869837e-03
## 25 12.226554 1.761932 0.4831390 3.956202 7.615075e-05 4.335474e-02
## 26 24.611005 -2.375353 0.4873701 -4.296872 1.732250e-05 2.074459e-02
## 27 121.712072 -1.696546 0.3771639 -4.464247 8.035091e-06 1.468688e-02
## 28 25.224328 -1.899884 0.4171767 -4.385883 1.155162e-05 1.745698e-02
## 29 3.965658 -1.921720 0.4684237 -4.004907 6.204187e-05 4.158190e-02
## 30 2823.645006 1.680737 0.4542890 4.208301 2.572978e-05 2.482138e-02
## 31 20.476808 -2.060546 0.4525946 -4.190209 2.786979e-05 2.535153e-02
## 32 15.860698 1.610399 0.4953808 4.097264 4.180629e-05 3.024772e-02
## 33 35.637218 -2.755400 0.4945205 -4.735731 2.182665e-06 7.580177e-03
## 34 12.587251 1.529453 0.4951569 4.552836 5.292742e-06 1.148823e-02
## 35 66.893717 -2.130275 0.4621906 -4.191116 2.775855e-05 2.535153e-02
## 36 35.360125 1.588949 0.3620402 4.320452 1.557101e-05 2.074459e-02
## 37 29.869426 1.882873 0.4861747 4.736973 2.169343e-06 7.580177e-03
## 38 23.497928 2.178703 0.4705782 5.045747 4.517523e-07 2.753122e-03
## 39 50.339796 -1.748053 0.4206420 -4.182062 2.888776e-05 2.535153e-02
## 40 154.506563 -1.781182 0.3991753 -4.385702 1.156125e-05 1.745698e-02
## 41 11.126036 1.882256 0.4284128 4.167825 3.075199e-05 2.535153e-02
## 42 19.153592 -3.024342 0.4942386 -4.694029 2.678766e-06 8.457352e-03
## 43 13.814454 -1.866275 0.4247947 -4.148790 3.342379e-05 2.579500e-02
## 44 7.344667 -1.866484 0.4524081 -4.249707 2.140506e-05 2.323052e-02
## gene symbol
## 1 ENSG00000007314.7 SCN4A
## 2 ENSG00000073754.5 CD5L
## 3 ENSG00000100413.12 POLR3H
## 4 ENSG00000104804.3 TULP2
## 5 ENSG00000108176.10 DNAJC12
## 6 ENSG00000108576.5 SLC6A4
## 7 ENSG00000115616.2 SLC9A2
## 8 ENSG00000118322.8 ATP10B
## 9 ENSG00000119660.3 RP11-293M10.4
## 10 ENSG00000124602.5 UNC5CL
## 11 ENSG00000125744.7 RTN2
## 12 ENSG00000130675.10 MNX1
## 13 ENSG00000135346.4 CGA
## 14 ENSG00000137571.6 SLCO5A1
## 15 ENSG00000162771.6 FAM71A
## 16 ENSG00000165462.5 PHOX2A
## 17 ENSG00000173080.4 RXFP4
## 18 ENSG00000173406.11 DAB1
## 19 ENSG00000182010.6 RTKN2
## 20 ENSG00000186007.5 LEMD1
## 21 ENSG00000198576.2 ARC
## 22 ENSG00000211638.2 IGLV8-61
## 23 ENSG00000213253.5 CTC-250I14.1
## 24 ENSG00000213386.3 RP11-779O18.2
## 25 ENSG00000221046.1 RNU6ATAC38P
## 26 ENSG00000228100.1 AC016912.3
## 27 ENSG00000228323.2 AC008753.6
## 28 ENSG00000228413.1 AC024937.2
## 29 ENSG00000229137.2 RP11-101P17.11
## 30 ENSG00000232931.1 LINC00342
## 31 ENSG00000233009.1 NALCN-AS1
## 32 ENSG00000239942.2 RN7SL394P
## 33 ENSG00000241458.1 RP11-461O14.1
## 34 ENSG00000242948.1 EPS15P1
## 35 ENSG00000244131.2 RPSAP51
## 36 ENSG00000253298.1 AC008703.1
## 37 ENSG00000253687.1 CTC-348L5.1
## 38 ENSG00000257443.1 RP11-150C16.1
## 39 ENSG00000259687.1 RP11-293M10.5
## 40 ENSG00000260908.1 CTB-134H23.3
## 41 ENSG00000262636.1 CTD-3088G3.4
## 42 ENSG00000264125.1 RP11-354P11.4
## 43 ENSG00000266120.1 RP11-354P11.2
## 44 ENSG00000273175.1 RP11-11N7.4x_upG <- x[which(x$log2FoldChange>0),"symbol"]
x_upP <- x[which(x$log2FoldChange<0),"symbol"]
x_upG## [1] DNAJC12 SLC9A2 ATP10B UNC5CL MNX1
## [6] SLCO5A1 LEMD1 RNU6ATAC38P LINC00342 RN7SL394P
## [11] EPS15P1 AC008703.1 CTC-348L5.1 RP11-150C16.1 CTD-3088G3.4
## 36664 Levels: 5S_rRNA 7SK A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 ... ZZZ3x_upP## [1] SCN4A CD5L POLR3H TULP2 SLC6A4
## [6] RP11-293M10.4 RTN2 CGA FAM71A PHOX2A
## [11] RXFP4 DAB1 RTKN2 ARC IGLV8-61
## [16] CTC-250I14.1 RP11-779O18.2 AC016912.3 AC008753.6 AC024937.2
## [21] RP11-101P17.11 NALCN-AS1 RP11-461O14.1 RPSAP51 RP11-293M10.5
## [26] CTB-134H23.3 RP11-354P11.4 RP11-354P11.2 RP11-11N7.4
## 36664 Levels: 5S_rRNA 7SK A1BG A1BG-AS1 A1CF A2M A2M-AS1 A2ML1 A2MP1 ... ZZZ3Pathway enrichment analysis fGSEA
CANARY Good prognosis (G) is the reference. When sample is P, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## ------------------------------------------- ---------- ---------- ----------- ---------- ------------- ----- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ------
## HALLMARK_E2F_TARGETS 0.0015337 0.0144092 0.5295767 2.464249 0 191 DCTPP1 HELLS PRIM2 NUP107 NME1 GINS1 CHEK2 TRIP13 CDK4 HMMR BUB1B CDCA8 UBE2T CDK1 E2F8 PTTG1 POLD2 RPA3 DEPDC1 CENPM LMNB1 PCNA TBRG4 CCNB2 RAD51AP1 RRM2 PAICS MCM4 TIPIN CDC25A SMC6 PPP1R8 MELK MKI67 PRKDC CCP110 PMS2 ASF1B RBBP7 SRSF1 EZH2 RAD50 RACGAP1 STMN1 CTPS1 KIF18B TCF19 MSH2 PRPS1 TOP2A GINS4 BRCA1 ESPL1 PRDX4 AURKB NUP205 PLK1 MCM5 AURKA ORC6 MAD2L1 MCM3 MYBL2 SRSF2 CHEK1 MTHFD2 PHF5A TP53 RAD1 MCM2 MMS22L HMGA1 POLA2 TIMELESS MCM7 POLD3 UBR7 KIF22 CKS1B HUS1 NCAPD2 KIF2C SPAG5 BARD1 RPA1 UNG RANBP1 NOLC1 RNASEH2A WDR90 EIF2S1 SPC24 CDKN3 SPC25 DCLRE1B ATAD2 SNRPB PLK4 RAN BIRC5 DSCC1 TUBG1 SMC4 PA2G4 CDC20 RAD51C CKS2 NAA38 XPO1 CCNE1 DLGAP5 MCM6 POLE ZW10 POP7 up
## HALLMARK_TGF_BETA_SIGNALING 0.0023641 0.0144092 -0.5643045 -2.265810 0 54 SMAD6 PPP1R15A SMAD7 LTBP2 CDKN1C ENG CDK9 SPTBN1 SKI BMP2 ID3 TGFB1 JUNB BMPR2 NOG BMPR1A TGIF1 ID2 RHOA TJP1 NCOR2 ID1 BCAR3 LEFTY2 THBS1 KLF10 down
## HALLMARK_MYOGENESIS 0.0028818 0.0144092 -0.4527237 -2.216635 0 190 VIPR1 TCAP SGCA AK1 CFD HBEGF MYO1C TNNC2 SGCG TNNC1 MYL3 CDH13 SORBS3 ACTN2 MYH11 FHL1 GPX3 FXYD1 SOD3 GAA MYLK SLN ACTN3 NOS1 NOTCH1 ANKRD2 PYGM TAGLN CD36 DES PTGIS SPTAN1 TGFB1 KIFC3 DMPK PPP1R3C TPM2 SMTN DAPK2 HDAC5 COX7A1 EFS CKM FOXO4 HSPB8 FKBP1B FGF2 CACNA1H ADCY9 ACTC1 IFRD1 PVALB SORBS1 CASQ2 CTF1 COL4A2 MYOZ1 MAPK12 BAG1 AEBP1 CACNG1 LDB3 COL6A2 ENO3 MYH2 TEAD4 OCEL1 REEP1 MYH9 FST MYL4 APOD CLU GJA5 DTNA PKIA MYL1 down
## HALLMARK_GLYCOLYSIS 0.0015314 0.0144092 0.4662648 2.171636 0 188 SOX9 B3GAT1 PKP2 GPR87 KIF2A SRD5A3 FUT8 ADORA2B PMM2 KIF20A COPB2 HMMR BIK POLR3K CASP6 GFPT1 CDK1 B3GNT3 ABCB6 DEPDC1 MERTK CENPA CHST4 EGFR PPIA FBP2 EFNA3 ANGPTL4 ANKZF1 TPBG SLC25A13 KDELR3 COG2 BPNT1 SDHC GAL3ST1 STMN1 PRPS1 CHST6 IER3 GALE RPE PKM CXCR4 ENO1 AURKA ELF3 AK4 SDC1 AGL ANG GMPPA FKBP4 TSTA3 SLC35A3 ALDH7A1 ALDOB TFF3 SLC25A10 SLC37A4 GAPDHS GOT2 ALDOA CLDN9 B4GALT4 PGAM1 ME2 NT5E PYGB HDLBP PSMC4 PC GNPDA1 HAX1 STC2 MIOX CHST2 PGM2 IDH1 PAXIP1 up
## HALLMARK_G2M_CHECKPOINT 0.0015221 0.0144092 0.4346215 2.026716 0 187 E2F3 EFNA5 PRIM2 NDC80 SLC12A2 TROAP STIL EXO1 CDK4 HMMR PBK TTK CENPF CDK1 NEK2 MNAT1 SLC38A1 PTTG1 UCK2 LMNB1 CENPA CCNB2 CDC6 E2F2 CDC25A MKI67 PRC1 NUSAP1 HIF1A SRSF1 EZH2 RACGAP1 LIG3 STMN1 TPX2 BUB1 HOXC10 EGF TOP2A FBXO5 ESPL1 CDC45 AURKB KIF23 PLK1 MCM5 AURKA ORC6 MAD2L1 MCM3 MYBL2 SRSF2 KIF11 CBX1 CHEK1 POLQ KIF15 MCM2 HMGA1 POLA2 SMARCC1 CDC7 KIF22 CUL3 CKS1B HUS1 SNRPD1 KIF2C KPNB1 TRAIP CCNF TOP1 SMAD3 SQLE BARD1 RBL1 BUB3 NOLC1 KIF20B RAD54L MTF2 CCND1 CDKN3 PLK4 CHAF1A BIRC5 ORC5 SMC4 CDC20 CKS2 XPO1 SLC7A5 MCM6 POLE HIRA up
## HALLMARK_MYC_TARGETS_V1 0.0015291 0.0144092 0.4335424 2.020142 0 189 CCT2 SRPK1 NME1 CDK4 ACP1 CBX3 CCT5 COPS5 CCT3 POLD2 VDAC1 ILF2 PCNA TYMS MCM4 PPIA HSP90AB1 PSMD1 GLO1 XPOT SSBP1 SRSF1 LSM7 HNRNPR AIMP2 PWP1 CTPS1 CCT4 ERH NPM1 PRDX4 MRPL9 CDC45 EIF3B FAM120A PHB MCM5 YWHAQ MAD2L1 CSTF2 SRSF2 RFC4 GNL3 SNRPB2 EEF1B2 RSL1D1 MCM2 RPS10 NHP2 PRPS2 MCM7 HSPE1 SMARCC1 NDUFAB1 HDGF DDX21 SNRPA PRDX3 HSPD1 SNRPD1 KPNB1 TARDBP GOT2 SNRPD2 ABCE1 SNRPG RANBP1 POLE3 BUB3 NOLC1 PSMB2 EIF2S2 CANX TXNL4A PSMC4 PSMB3 CDK2 EIF2S1 HNRNPC CCT7 CAD PSMC6 APEX1 RAN PSMA4 UBA2 COX5A PA2G4 CDC20 DHX15 LDHA XPO1 RRM1 MCM6 PSMA6 DDX18 EIF3J HNRNPA2B1 SERBP1 PSMD8 CCNA2 PPM1G SNRPA1 NOP56 G3BP1 HDAC2 PABPC1 RUVBL2 SF3B3 PTGES3 UBE2L3 AP3S1 SSB FBL PSMA1 TUFM YWHAE SNRPD3 HNRNPD NCBP2 EIF4G2 PABPC4 PSMA2 up
## HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0028653 0.0144092 -0.3905184 -1.921459 0 195 SIK1 EGR2 PPP1R15A NR4A1 JUN EGR1 PER1 FOSB KLF4 HBEGF IER2 GEM KLF6 PNRC1 ZFP36 RHOB CEBPD BMP2 KLF2 OLR1 IRS2 DUSP1 FOS PTGER4 ATF3 CCNL1 NFKBIA JUNB EIF1 NR4A2 GFPT2 STAT5A KLF9 MAP3K8 TGIF1 RCAN1 CXCL3 MCL1 INHBA ID2 MAFF DENND5A IRF1 CEBPB SOCS3 BTG2 TNIP2 IL18 ETS2 KDM6B CCRL2 DRAM1 PTPRE NR4A3 ABCA1 CXCL2 MSC TRIB1 TIPARP TNFSF9 DNAJB4 IFIT2 KLF10 MAP2K3 CD83 ACKR3 TSC22D1 EHD1 TNFAIP2 NFKB2 BTG1 CD80 CD44 IER5 down
## HALLMARK_MYC_TARGETS_V2 0.0017153 0.0144092 0.4458426 1.727976 0 57 DCTPP1 SORD CDK4 CBX3 WDR43 TBRG4 MCM4 SLC29A2 AIMP2 UTP20 NOP2 NPM1 PHB PLK1 MCM5 GNL3 HSPE1 MPHOSPH10 SUPV3L1 HSPD1 UNG NOLC1 TFB2M PLK4 up
## HALLMARK_UV_RESPONSE_DN 0.0026882 0.0144092 -0.3650163 -1.698037 0 136 CITED2 BDNF NR3C1 PTPN21 GRK5 DLC1 SMAD7 TGFBR3 RXRA PTPRM ZMIZ1 CAV1 TGFBR2 DUSP1 AKT3 DYRK1A PPARG LTBP1 BMPR1A APBB2 KIT PEX14 NEK7 INSIG1 SYNE1 FZD2 TJP1 CDKN1B SPOP PRKCE DAB2 ATXN1 ATP2B4 ID1 MAP2K5 CDON PHF3 KCNMA1 TFPI PMP22 WDR37 MAGI2 FBLN5 CELF2 VAV2 PIK3CD PRKAR2B PDGFRB PTGFR RBPMS DBP MT1E VLDLR PTEN down
## HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0028736 0.0144092 -0.3290354 -1.608352 0 189 CRLF1 BDNF JUN NTM SGCG TGFBR3 GEM BMP1 RHOB PCOLCE2 MYLK SFRP4 FSTL3 TAGLN TGFB1 SLIT2 TIMP3 MYL9 TPM2 LRP1 INHBA EFEMP2 ID2 FGF2 ITGA5 EDIL3 ABI3BP ACTA2 DAB2 GAS1 VIM FOXC2 IGFBP2 COL4A2 WNT5A FERMT2 CADM1 SFRP1 COL6A2 FBLN1 CALD1 THBS1 PMP22 NNMT FBLN5 SLIT3 LAMA3 GREM1 MMP2 EMP3 THBS2 PDGFRB SCG2 CD44 COL8A2 CAPG LOXL1 VEGFA TGM2 VEGFC FN1 down
## HALLMARK_APICAL_JUNCTION 0.0057471 0.0234880 -0.3117463 -1.523842 1 189 TSPAN4 MYH10 RRAS BMP1 SORBS3 ACTN2 EPB41L2 PECAM1 CLDN5 MSN ACTN3 FLNC PKD1 AKT3 JAM3 ITGA9 PARVA SLIT2 MYL9 VWF NEXN BAIAP2 ARHGEF6 GNAI2 ACTG2 ICAM2 TSC1 AMIGO1 ZYX SIRPA MAP4K2 MVD INSIG1 CNN2 ACTC1 TJP1 LAYN CDH15 EVL NF2 VASP THBS3 GAMT STX4 MAPK11 CDSN ADAMTS5 MYH9 NLGN3 LAMA3 MMP2 RHOF VAV2 down
## HALLMARK_ADIPOGENESIS 0.0056657 0.0234880 -0.3118041 -1.517354 1 183 ACO2 SOWAHC SLC19A1 GPX3 CAT MYLK FZD4 NKIRAS1 SULT1A1 CD36 RMDN3 QDPR LIFR ALDH2 PPARG FABP4 CYP4B1 EPHX2 ITIH5 STAT5A RETN LPL HSPB8 ACADL PEX14 LTC4S VEGFB CD151 AGPAT3 SORBS1 PGM1 PHLDB1 LAMA4 MARC2 DBT PEMT PTGER3 PFKL ADIPOR2 ABCA1 ANGPT1 RREB1 ARAF SPARCL1 UCK1 CPT2 CD302 PIM3 BCKDHA PPP1R15B down
## HALLMARK_MTORC1_SIGNALING 0.0061069 0.0234880 0.3204568 1.491929 3 190 ELOVL6 SRD5A1 SORD DHFR ELOVL5 TCEA1 SYTL2 COPS5 EEF1E1 CCT6A LGMN RRM2 MCM4 PPIA CDC25A PDK1 GMPS GAPDH TRIB3 YKT6 BUB1 PSPH HSPA9 PSAT1 CXCR4 ENO1 NUP205 PLK1 AURKA SHMT2 AK4 PITPNB MTHFD2 MCM2 HSPE1 DAPP1 PPA1 DDIT3 HSPD1 PNP ACLY CCNF SLC37A4 TES PSME3 HSPA4 ALDOA TBK1 RIT1 SQLE SLC1A4 RPA1 UNG PHGDH EIF2S2 CANX PSMC4 CCNG1 XBP1 SLC2A1 IDH1 ADD3 PSMC6 GSR PSMB5 TUBG1 DDIT4 PSMA4 EGLN3 GPI GCLC PIK3R3 LDHA STIP1 SLC7A5 PSMA3 SLC9A3R1 UCHL5 RAB1A FDXR FADS2 SERP1 NFYC ASNS CTH P4HA1 RPN1 NUFIP1 TM7SF2 TXNRD1 BHLHE40 up
## HALLMARK_PROTEIN_SECRETION 0.0085763 0.0306297 0.3544445 1.474694 4 89 TSPAN8 ICA1 COPB2 BET1 TPD52 ARFGAP3 EGFR AP2B1 DNM1L COG2 ARFGEF1 YKT6 KRT18 TOM1L1 TMED2 SEC24D RPS6KA3 RAB9A LMAN1 CLTC MON2 SCRN1 AP3B1 RER1 COPB1 RAB22A TMED10 GOSR2 VPS45 ARFIP1 ZW10 TSG101 up
## HALLMARK_XENOBIOTIC_METABOLISM 0.0114613 0.0382044 -0.2927439 -1.432092 3 188 ACO2 ABCC2 CYP17A1 RBP4 PMM1 SLC12A4 TTPA ALAS1 PINK1 CAT CYP27A1 CYP1A2 CD36 SLC6A12 HMOX1 PAPSS2 GNMT ALDH2 FBP1 LPIN2 LEAP2 F10 MAN1A1 ABHD6 PDK4 F11 COMT ACOX3 CDO1 TGFB2 ID2 GABARAPL1 HSD11B1 ACSM1 DCXR LCAT ETS2 CES1 MT2A ADH5 PEMT IGFBP1 ATOH8 SLC22A1 NDRG2 MPP2 PTS GCNT2 FBLN1 HNF4A SERTAD1 HACL1 PROS1 GSTO1 TYR ITIH4 SLC6A6 ARG1 down
fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## --------- ---------- --------- ----------- ---------- ------------- ----- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ------
## chr3p21 0.0028409 0.024599 -0.5259742 -2.642284 0 211 SEMA3G RNU5B-3P MIR425 LIMD1 CCDC36 CLEC3B IL17RB MIR191 ABHD5 TGM4 ARIH2OS SEMA3B PTH1R TNNC1 MYL3 CACNA2D2 ALAS1 LAMB2 LIMD1-AS1 MAP4 MIR138-1 IP6K1 RNA5SP131 TMIE MIRLET7G RN7SL182P C3orf62 GPR62 SCAP PPM1M DALRD3 MUSTN1 BAP1 LRRC2 GMPPB SLC25A20 RAD54L2 GNAI2 RPS24P8 ZNF445 UBA7 CAMP TMEM115 TREX1 ALS2CL ANO10 NISCH FCF1P2 TLR9 CHDH DCP1A PCBP4 ZNF197 FYCO1 C3orf84 PHF7 NRADDP RASSF1 RHOA NCKIPSD ZNF35 NME6 ABHD14A-ACY1 USP4 NPRL2 ABHD14A ARIH2 ZNF660 SNORD69 ITIH3 CCRL2 FBXW12 CCDC71 KLHDC8B WDR82 NDUFAF3 SNORD19B SACM1L RHOA-IT1 USP19 TOPAZ1 ZNF501 MON1A SETD2 WDR6 NICN1 PTPN23 CCDC12 TCTA SEMA3F MPRIPP1 RNF123 KIF9-AS1 DHX30 QRICH1 ITIH4 KLHL18 PBRM1 ACTR8 DUSP7 PRKAR2A BSN down
## chr12q15 0.0017825 0.024599 0.7543284 2.556305 0 34 FAHD2P1 RN7SL804P CPSF6 IL26 CCT2 YEATS4 NUP107 MYRFL MDM1 RAB3IP PRELID2P1 IL22 KRT8P39 IFNG-AS1 MRPL40P1 MDM2 FRS2 CNOT2 HNRNPA1P70 SLC35E3 PTPRR RAP1B SNORA70G BEST3 IFNG DYRK2 RPL39P28 up
## chr17p13 0.0028736 0.024599 -0.4766214 -2.433883 0 236 ZBTB4 INPP5K TLCD2 ARHGEF15 KIF1C MYH10 ASGR1 GLTPD2 RILP PER1 MYO1C SENP3-EIF4A1 SCARF1 ZMYND15 SAMD11P1 ALOX12B VAMP2 MIR132 TNFSF12 MED11 HIC1 MIR212 EIF4A1 TIMM22 MIR497HG CXCL16 NLRP1 ELP5 MINK1 TNFSF13 SLC35G6 MIR22HG SMG6 C17orf49 ZZEF1 SMYD4 TMEM88 PAFAH1B1 SLC16A11 SENP3 SAT2 ANKFY1 ARRB2 RNASEK USP6 SPAG7 FXR2 MIR324 VMO1 NDEL1 SOX15 WDR81 HES7 TMEM256-PLSCR3 TMEM95 DLG4 KCTD11 ATP1B2 KDM6B TMEM220 SLC43A2 TRPV1 GPS2 DPH1 CYB5D2 RPH3AL ABR SLC25A11 TM4SF5 PIK3R5 ATP6V0CP1 RN7SL608P WSCD1 CHRNE ADPRM C17orf107 BCL6B ENO3 GLP2R RPL7AP64 SLC13A5 PITPNA PLD2 MYH2 RANGRF SMTNL2 PIK3R6 ASPA METTL16 CNTROB RN7SL774P PRPF8 SHPK CAMTA2 SERPINF2 EMC6 CAMKK1 MIR3183 GP1BA down
## chr7p21 0.0016639 0.024599 0.6531595 2.386030 0 45 ITGB8 COL28A1 MIOS SCIN BZW2 MACC1-AS1 ICA1 VWDE PHF14 AGR2 AHR RBMX2P4 MACC1 RPA3 RN7SKP266 AGMO TMEM106B TWISTNB TAS2R2P RN7SKP228 ANKMY2 NXPH1 ABCB5 TMEM196 HDAC9 SP8 NDUFA4 up
## chr13q33 0.0022779 0.024599 -0.6193285 -2.267615 0 35 LINC00443 LINC00551 RNY1P2 METTL21C FGF14-AS1 FGF14-AS2 FGF14-IT1 ARGLU1 NALCN RPL39P29 ITGBL1 BIVM LIPT1P1 TEX30 EFNB2 FGF14 MIR4705 MYO16-AS1 HMGB3P7 ERCC5 CCDC168 RNU1-24P TPP2 MYO16 down
## chr3p22 0.0024155 0.024599 -0.4805543 -2.236764 0 118 VIPR1 TRIM71 CSRNP1 TTC21A STAC SCN5A PLCD1 VIPR1-AS1 GORASP1 SEC22C RNU7-73P DDTP1 ITGA9 XIRP1 TMPPE ZBTB47 RPL21P135 EXOG CRTAP NDUFAF4P3 MYD88 UBP1 UBE2FP1 CLASP2 SNRK SLC25A38 WDR48 ACVR2B GPD1L ACAA1 SUSD5 PDCD6IP GLB1 SNRK-AS1 CTDSPL down
## chr9q34 0.0028571 0.024599 -0.4451741 -2.229517 0 210 ST6GALNAC6 SH2D3C CLIC3 RNA5SP296 LAMC3 AK1 MIR126 ENG EGFL7 CDK9 FAM166A RXRA ADAMTSL2 ST6GALNAC4 EXD3 NOTCH1 HMCN2 MIR4672 DNLZ MIR4669 SPTAN1 UAP1L1 CACFD1 GPSM1 BARHL1 EEF1A1P5 TSC1 SLC25A25 NACC2 RN7SL665P RAPGEF1 QRFP MAMDC4 PPP1R26 PKN3 TBC1D13 NTNG2 FBXW5 LINC00963 INPP5E MIR4479 DPP7 TOR2A PMPCA ENDOG GFI1B PHYHD1 PNPLA7 C8G FPGS TUBB4B RALGDS LCNL1 FCN2 BRD3 MRPL41 POMT1 SARDH MIR4292 FAM78A FAM163B SNHG7 C9orf106 ABL1 ZER1 SSNA1 TRAF2 ABCA2 VAV2 PRRC2B UCK1 NCLP1 NELFB ANAPC2 CARD9 PTGDS DBH MIR3911 LCN15 USP20 PHPT1 C9orf139 CAMSAP1 TPRN SLC27A4 NSMF CIZ1 SETX EHMT1 TTF1 PAEP RABL6 TOR4A PIP5KL1 FCN1 down
## chr13q34 0.0024155 0.024599 -0.5396746 -2.152492 0 54 GAS6 CARS2 LINC00346 IRS2 LINC01070 ING1 LAMP1 LINC00396 F10 DCUN1D2-AS RASA3 DCUN1D2 GAS6-AS1 TMEM255B ATP11A LINC00452 ATP4B COL4A2 ANKRD10 RASA3-IT1 TUBGCP3 COL4A2-AS2 UPF3A TEX29 MCF2L ARHGEF7 CUL4A ATP11A-AS1 RNU1-16P CDC16 down
## chr7p22 0.0016502 0.024599 0.5176545 2.117685 0 85 ZDHHC4 C1GALT1 ZNF12 KDELR2 OR7E136P CCZ1B FAM220A GET4 EIF2AK1 SLC29A4 RNF216P1 LFNG ANKRD61 RBAK RAC1 GRID2IP PMS2CL CCZ1 ALG1L5P MIR4648 CARD11 SUN1 PMS2 OCM UNC93B2 AIMP2 NUDT1 RN7SKP130 IQCE USP42 TTYH3 ADAP1 EIF3B TMEM184A ZNF890P RSPH10B2 COX19 RNF216 WIPI2 FAM86LP DAGLB BRAT1 up
## chr12q14 0.0017036 0.024599 0.5522106 2.108102 0 56 GRIP1 LRIG3 HMGA2 PPM1H OSBPL9P4 METTL1 RPL32P26 GAPDHP44 C12orf66 SLC16A7 CDK4 KLF17P1 HELB AVIL CAND1 TSFM C12orf56 GGTA2P RPSAP52 XPOT TSPAN31 LLPH LEMD3 AVPR1A USP15 TBK1 MON2 CTDSP2 DPY19L2 CYP27B1 up
## chr17q23 0.0023256 0.024599 -0.4925407 -2.058846 0 64 SCN4A TBX2 ACE TUBD1 C17orf82 TBX4 NDUFB8P2 CA4 RN7SL606P PECAM1 PPM1D POLRMTP1 TEX2 ICAM2 RNU6-446P MAP3K3 down
## chr16q24 0.0024938 0.024599 -0.4643433 -2.056095 0 92 WFDC1 FOXF1 FENDRR PABPN1L MIR5093 LINC01081 LINC00311 PIEZO1 SPATA2L ZCCHC14 SNAI3 MVD IL17C CBFA2T3 SNAI3-AS1 CDH15 TUBB3 FOXC2 ATP2C2 RNF166 KLHL36 DEF8 MIR5189 GSE1 CYBA KIAA0513 TAF1C AFG3L1P ZNF276 CDK10 C16orf95 ZNF469 COTL1 MTHFSD FBXO31 ANKRD11 CTU2 MBTPS1 RPL13 MC1R CPNE7 CHMP1A TCF25 SLC22A31 ZC3H18 MAP1LC3B LINC00304 down
## chr15q11 0.0023529 0.024599 -0.4807812 -1.998674 0 63 SNORD116-3 WHAMMP3 SNORD116-1 HERC2P3 SNORD116-8 SNORD116-5 SNORD116-18 SNORD116-12 SNORD116-16 NF1P1 SNORD116-2 NF1P2 NPAP1 SNORD116-23 SNORD108 SNORD116-19 PWRN2 SNORD116-17 PWRN1 SNORD116-7 SNORD109A NBEAP1 MIR3118-3 SNORD116-11 SNHG14 SNORD116-24 SNORD116-20 NDN SNRPN SNORD116-30 SNURF SNORD116-6 SNORD116-9 GRAMD4P6 SNORD116-14 SNORD64 SNORD116-15 SNORD116-29 SNORD116-26 SNORD116-13 CYFIP1 SNORD116-27 down
## chr14q23 0.0016611 0.024599 0.4925787 1.995185 0 77 SYT16 SALL4P7 SIX6 SIX1 RPL21P8 EIF1AXP2 FUT8 RPL21P7 HNRNPCP1 C14orf39 SIX4 GPX2 MNAT1 SNAPC1 SRMP2 PTBP1P HIF1A LRRC9 HMGB1P14 LINC00643 SPTB TEX21P MIR625 MTHFD1 TMEM30B RNU6-1162P RAB15 L3HYPDH HIF1A-AS1 RNU6-597P FNTB CCDC175 MIR548H1 EIF2S1 JKAMP TIMM9 PPP2R5E DHRS7 ESR2 SLC35F4 KIAA0586 SYNE2 PSMA3 WDR89 RPL9P5 up
## chr12p11 0.0017153 0.024599 0.5363620 1.911814 0 41 PKP2 DDX11-AS1 BICD1 AK4P3 DDX11 MRPS35 DENND5B ARNTL2 SYT10 TM7SF3 AMN1 LINC00941 MANSC4 STK38L DNM1L RNU6-494P PTHLH ALG10 YARS2 CAPRIN2 RNU6-1069P ERGIC2 RNU4-54P CCDC91 SMCO2 up
## chr1q21 0.0015175 0.024599 0.4047732 1.896220 0 191 RNU6-1042P PEX11B PGLYRP4 DCST1 S100A7 PGLYRP3 MIR554 GOLPH3L TCHHL1 TUFT1 SPRR3 SPRR2A THEM4 OR13Z2P HORMAD1 ANKRD34A EFNA4 C1orf56 TDRKH CREB3L4 SPRR1A FLAD1 ILF2 HYDIN2 PIP5K1A DCST2 SNX27 ACP6 EFNA3 S100A11 S100A16 VPS72 SPRR1B PIAS3 MIR4258 S100A6 SPRR2F UBE2Q1-AS1 RPRD2 TARS2 S100A5 MRPL9 NBPF9 RN7SL44P KRT8P28 LINC00624 S100A9 PSMD4 C2CD4D PSMB4 THEM5 POGZ OAZ3 LYSMD1 CKS1B MRPS21 CDC42SE1 RNVU1-7 SETDB1 SNAPIN C1orf43 SCNM1 CGN ADAM15 RNU6-1171P PFN1P6 RNF115 S100A13 HAX1 RBM8A RFX5 RAB13 S100A10 BCL9 NBPF18P CELF3 PYGO2 GPR89A CHTOP VPS45 S100A2 UBE2Q1 TCHH CHD1L TPM3 FMO5 CA14 RPS27 ADAR ANP32E IVL POLR3C up
## chr7q11 0.0016639 0.024599 0.4609246 1.880015 0 81 ZNF107 SKP1P1 ERV3-1 RPL35P5 ZNF117 PMS2P5 FDPSP7 ZNF92 ZNF273 ZNF138 VN1R42P ZP3 FDPSP2 STAG3L2 DTX2 KCTD7 LINC00174 SNORA22 GTF2IRD2 TYW1B PMS2P11 PMS2P2 TYW1 DTX2P1 TMEM60 GUSBP6 CCDC146 STAG3L4 POM121 POM121B VKORC1L1 POM121C STAG3L1 SPDYE9P NMD3P1 STAG3L3 TPST1 NSUN5P2 YWHAG FGL2 SEPHS1P1 GTF2IRD2B CCT6P3 NSUN5 GTF2IRD1 NCF1 PMS2P4 NSUN5P1 up
## chr11p11 0.0023923 0.024599 -0.4457377 -1.868691 0 66 FAM180B C11orf94 C11orf96 LRP4 PRDM11 RN7SL652P LRP4-AS1 CRY2 C1QTNF4 TSPAN18 SPI1 MAPK8IP1 KBTBD4 ARFGAP2 RPL34P22 RAPSN PHF21A CHST1 CD82 ALKBH3-AS1 PACSIN3 SEC14L1P1 PTPMT1 SLC39A13 ARHGAP1 F2 ALKBH3 MADD DGKZ PEX16 NR1H3 down
## chr5q13 0.0016892 0.024599 0.4614827 1.828830 0 70 ANKDD1B CENPH MCCC2 CRHBP UTP15 FAM169A POC5 CCNB1 ENC1 NSA2 GFM2 SV2C HMGN2P4 ANKRA2 MRPS27 BTF3 ARHGEF28 F2RL1 ANKRD31 CFL1P5 TMEM171 TAF9 PTCD2 MAP1B RNU7-196P GTF2H2C SLC30A5 CCDC125 S100Z SMN2 TNPO1 MARVELD2 AGGF1 up
## chr4p16 0.0024155 0.024599 -0.3918351 -1.823816 0 118 PDE6B WFS1 RNA5SP152 ADD1 CRMP1 DRD5 HTT-AS EVC HTT RNU6-204P SLC2A9 TMEM129 ACOX3 GPR78 NAT8L MXD4 TADA2B MYL5 AC097381.1 FAM86KP LRPAP1 TNIP2 MFSD10 NOP14-AS1 MIR3138 FGFR3 EVC2 GRK4 MAN2B2 RNA5SP155 HAUS3 CTBP1 DGKQ RGS12 ADRA2C ZFYVE28 FGFRL1 SH3TC1 ENPP7P9 TRMT44 CPZ CCDC96 SORCS2 SH3BP2 MSANTD1 WDR1 MRFAP1 TBC1D14 UVSSA IDUA TMEM128 LETM1 GAK down
## chr2q12 0.0034662 0.024599 0.5377123 1.796617 1 30 SLC9A2 SULT1C3 TMEM182 SLC9A4 MRPS9 SULT1C2 FHL2 GCC2 MFSD9 IL1RL2 POU3F3 up
## chr1q32 0.0015601 0.024599 0.3880431 1.788327 0 174 LEMD1 MROH3P LEMD1-AS1 CR2 ASCL5 TNNI1 MYBPH LAD1 RNU6-704P SYT14 FLVCR1 HHAT SERTAD4 FCAMR PROX1-AS1 RNU6-418P SNRPE LINC00467 TNNT2 KLHDC8A UBE2T SNRPGP10 RN7SL344P NEK2 IL10 PLEKHA6 IL24 KIF14 LPGAT1 TRAF5 PIGR IL20 LINC00862 DTL IL19 SNX25P1 RNU2-19P IRF6 PROX1 SLC45A3 KDM5B MIR205HG TIMM17A HNRNPA1P59 ELK4 RABIF IPO9 ELF3 up
## chr8p21 0.0025126 0.024599 -0.4053531 -1.777783 0 88 PEBP4 SCARA3 CHRNA2 BMP1 SORBS3 PDLIM2 PHYHIP DOK2 ADRA1A DPYSL2 LGI3 COX6B1P4 EPHX2 RNU6-892P NEFL C8orf58 NUDT18 LPL GULOP ZNF395 SFTPC TRIM35 CCAR2 RHOBTB2 DOCK5 GNRH1 HMBOX1 DMTN KCTD9 FGF17 ATP6V1B2 R3HCC1 CLU LZTS1 MIR320A PPP3CC GFRA2 NKX3-1 POLR3D PIWIL2 CSGALNACT1 BNIP3L down
## chr5q14 0.0016892 0.024599 0.4482264 1.776296 0 70 ACOT12 DHFR TBCA MTX3 COX7C RNU6-606P CKMT2-AS1 THBS4 RN7SL378P PPIAP11 TMEM161B LUCAT1 TMEM161B-AS1 COQ10BP2 TMEM167A ANKRD34B RAB5CP2 LINC00461 ATG10-AS1 XRCC4 CKMT2 RASA1 MEF2C MSH3 MBLAC2 ARRDC3 RNU4-90P AP3B1 RNA5SP187 SERINC5 up
## chr3p23 0.0018657 0.024599 0.8242501 1.770208 0 6 ZNF860 ZNF587P1 OSBPL10-AS1 up
## chr6p12 0.0017271 0.024599 0.4564207 1.758072 0 61 FAM83B C6orf141 PKHD1 CD2AP TINAG TNFRSF21 ELOVL5 KLHL31 RN7SL580P MLIP-IT1 MLIP-AS1 GCM1 CRISP3 PAQR8 MCM3 CENPQ CRISP2 MLIP HMGB1P20 EFHC1 GCLC TMEM14A ICK IL17A ANKRD66 RCC2P7 PTCHD4 RCAN2 MEP1A ZNF451 RN7SKP116 GLYATL3 RN7SK BMP5 LRRC1 PLA2G7 up
## chr7p15 0.0017271 0.024599 0.4486993 1.728330 0 61 HOXA11-AS DNAH11 HOXA10 OSBPL3 RNA5SP227 HOXA13 EVX1 MPP6 HOXA11 CBX3 TAX1BP1 STK31 CDCA7L FAM221A SP4 EIF4HP1 HIBADH HOXA9 IGF2BP3 PSMC1P2 NPY MALSU1 NFE2L3 TOMM7 CREB5 up
## chr11q23 0.0024938 0.024599 -0.3795620 -1.721529 0 105 SIDT2 FXYD2 DIXDC1 TREH FXYD6 APOA5 APOA1 BACE1 TAGLN SCN4B GRIK4 SIK2 TEX12 MRPS36P4 MCAM SCN2B LAYN PHLDB1 IL18 SC5D RBM7 CADM1 ST13P10 NXPE2P1 ZBTB16 NLRX1 TBCEL PTS DSCAML1 CBL TECTA NNMT C2CD2L RPS6P16 NXPE1 RN7SKP273 ARHGAP20 RNF214 down
## chr12p12 0.0034904 0.024599 0.4409620 1.712473 1 65 PIK3C2G PLCZ1 GUCY2C CAPZA3 PSMC1P9 PLEKHA5 RN7SL459P LDHB EPS8 RNU6-251P RNU1-146P EEF1A1P16 KRAS C12orf77 RERGL IAPP CMAS SLCO1B3 MGST1 RN7SL67P TUBB4BP1 CASC1 up
## chr2p11 0.0033389 0.024599 0.3995081 1.702669 1 113 IGKV1-9 IGKV1-8 IGKV2D-30 IGKV2D-29 IGKV1-17 IGKV1D-27 IGKV2-24 IGKV2-30 IGKV3OR2-268 IGKV2D-24 IGKV1-27 IGKV1D-12 IGKV1D-8 MAT2A RGPD2 IGKV5-2 IGKV3D-7 IGKV1-6 IGKV6D-21 IGKV2-26 EIF2AK3 IGKV3D-15 RNF103 IGKV1D-13 IGKJ3 IGKV3-11 GGCX IGKV3D-11 USP39 LDHAP7 IGKV1D-39 IGKV1-16 IGKV2D-28 ANKRD36BP2 IGKV1D-33 MRPL35 PTCD3 DNAH6 IGKV3D-20 IGKJ5 IGKV3-7 RGPD1 RETSAT IGKV7-3 POLR1A MTATP8P2 ANAPC1P1 IGKV3-20 IGKV1D-16 IGKV3-15 IGKV2-18 KDM3A RPL12P18 RNF181 KRCC1 MRPL45P1 IGKV1-5 IGKV2D-26 VAMP8 up
fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## ----------------------------------------------------- ---------- ---------- ----------- ---------- ------------- ----- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------
## ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER 0.0015798 0.0317567 0.6421310 2.830759 0 130 HELLS MCM10 NDC80 GINS1 KIF20A HJURP APOBEC3B DHFR STIL PAQR4 DNA2 TRIP13 FOXM1 HMMR PBK BUB1B CDCA8 TTK CENPF CDK1 E2F8 NEK2 SLC38A1 PTTG1 CCNB1 RPA3 CENPM KIF14 FANCI LMNB1 CENPA GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT CDC6 RRM2 MCM4 ASPM DSG2 GTSE1 MELK MKI67 PRC1 ASF1B NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 TPX2 PAFAH1B3 KIF18B BUB1 NETO2 TOP2A CEP55 GINS4 BRCA1 FBXO5 ESPL1 AURKB SPDL1 KIF23 PLK1 AURKA MAD2L1 MYBL2 KIFC1 KIF11 CHEK1 POLQ KIF15 MCM2 HMGA1 POLA2 MRPS15 NCAPG KIF2C CCNF SPAG5 up
## PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN 0.0024691 0.0317567 -0.7333366 -2.767269 0 38 RASL12 GRK5 ID4 MYLIP PRELP TNS1 PKIG CPED1 EMP2 MYH11 SOD3 MYLK JAM3 PTGIS LMOD1 KCNMB1 FIBIN SYNPO2 CRIM1 PKD2 ADCY9 SUSD5 ACTC1 RABGAP1 HSPB1 down
## SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP 0.0015552 0.0317567 0.6183624 2.759435 0 138 LAGE3 MCM10 BLM NDC80 NME1 GINS1 KIF20A HJURP APOBEC3B MRPL15 TROAP STIL EXO1 TRIP13 FOXM1 HMMR BUB1B CDCA8 TTK CCT5 CENPF CDK1 E2F8 NEK2 PTTG1 CCNB1 PARPBP KIF14 LMNB1 CENPA CCNB2 ZWINT RRM2 MCM4 CDC25A ASPM GTSE1 MELK MKI67 GMPS PRC1 XPOT GTPBP4 NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 STMN1 TPX2 KIF18B NUDT1 BUB1 TOP2A CEP55 FBXO5 ESPL1 ORMDL2 CMC2 CDC45 AURKB POLR2K PLK1 AURKA MIS18A MAD2L1 SHMT2 MCM3 MYBL2 KIFC1 KIF11 RFC4 CHEK1 POLQ KIF15 MCM2 TIMELESS DNAJC9 HCCS RAD54B NCAPG KIF2C SPAG5 SNRPG QPRT CENPI SNRPC RNASEH2A FEN1 CDK2 CDKN3 PKMYT1 BIRC5 DSCC1 CDC20 CKS2 NCAPG2 DLGAP5 STIP1 SLC7A5 MCM6 RAD51 TIMM10 TUBA1C TXN E2F1 UBE2S ITCH CCNA2 up
## KOBAYASHI_EGFR_SIGNALING_24HR_DN 0.0015060 0.0317567 0.5613808 2.705779 0 239 TCN1 SOX9 DKK1 EREG HMGA2 TFPI2 HELLS ADORA2B MCM10 BLM NDC80 NME1 GINS1 HJURP DHFR STIL EXO1 TRIP13 HMMR PBK BUB1B POLR3K CDCA8 TTK CDK1 E2F8 NEK2 EEF1E1 TUBB2A CCNB1 DEPDC1 UCK2 CENPM KIF14 CKLF DCBLD2 FANCI LMNB1 STEAP1 CENPA GALNT10 GMNN PCNA DTL PUS7 TYMS RAD51AP1 ZWINT CDC6 RRM2 PAICS MCM4 TIPIN CDC25A ASPM GTSE1 MELK MKI67 PRC1 ASF1B GPSM2 NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 CTPS1 TPX2 KIF18B MSH2 BUB1 ORC1 PRPS1 NETO2 TOP2A CEP55 IER3 BRCA1 PSAT1 SLC20A1 ESPL1 CMC2 CDC45 AURKB HSPA14 SPDL1 KIF23 PLK1 MCM5 AURKA ORC6 MAD2L1 CARD10 MCM3 MYBL2 KIF11 RFC4 DUSP5 KIF15 NOC3L FAM86C1 MCM2 ITGA6 PRIM1 POLA2 GJB3 TIMELESS MCM7 POLR2D DNAJC9 RMI1 RAD54B CKS1B MSH6 NCAPG SNRPD1 KIF2C CCNF CDT1 POLE2 SPAG5 ABCE1 SPRED2 BARD1 UNG SLCO4A1 RANBP1 UPP1 NOLC1 CDC42EP1 NT5E RNASEH2A FEN1 ZWILCH CCND1 CDK2 RFWD3 CDKN3 SPC25 RRP15 ATAD2 PLK4 ERCC6L CHAF1A PKMYT1 BIRC5 DSCC1 TUBG1 SMC4 PA2G4 CDC20 CKS2 NCAPG2 NCAPD3 DLGAP5 RRM1 MCM6 HAT1 up
## VANHARANTA_UTERINE_FIBROID_DN 0.0026178 0.0317567 -0.6447834 -2.683205 0 61 CITED2 NR3C1 SMAD7 EGR1 GIMAP6 KLF4 IER2 CBX7 PHYHIP ODC1 HOXA5 GATA2 KLF2 APOL3 WFS1 SOX17 GSTM5 ATF3 RARRES2 LTBP1 PTCH1 NR4A2 DAPK1 MAFF ABCA8 ADH1B PTGER3 TFPI TRIB1 LEPR ACKR3 C1R down
## WONG_ENDMETRIUM_CANCER_DN 0.0026810 0.0317567 -0.6220488 -2.674710 0 76 LTBP4 TBX3 MASP1 GAS6 DPP6 EDNRB WNT4 LDB2 JPH4 RUNX1T1 HIC1 SFRP4 LMOD1 KIF26A F10 MME TSHZ3 CTSW SYNPO2 PID1 PDGFRA COX7A1 PEG3 EHD2 XYLT1 EFS SLC24A3 CNRIP1 GNLY MICU3 VGLL3 EMILIN1 TWIST2 SLC18A2 TCEAL7 ADAMTS5 down
## VECCHI_GASTRIC_CANCER_EARLY_UP 0.0014025 0.0317567 0.5070409 2.577733 0 403 ATP10B SLC4A11 MYEOV TMEM45B ILDR1 NUP62CL CLDN2 GUCY2C KCNN4 E2F7 TMC5 CLDN1 LACTB2 LCN2 HOXA10 CENPH ITGA2 CENPK ADORA2B ZNF117 MCM10 TMPRSS4 CDCA7 PMS2P5 FERMT1 STRIP2 NDC80 PDP1 MUC13 DEPDC1B TM4SF1 C12orf66 NME1 CDH17 GINS1 MMP7 KIF20A NUP155 DHFR FIGNL1 PDCD6 TRIP13 EFNA4 FOXM1 HMMR PBK BUB1B ANLN PI3 TTK SATB2-AS1 UBE2T CENPF CDK1 E2F8 MACC1 NEK2 NUF2 XPO5 RP9 CLRN3 PTTG1 CCT3 CCNB1 RPA3 DEPDC1 PARPBP TRMT6 CENPM KIF14 FANCI ZIC2 CENPA SEMA4B DTL PUS7 LAMC2 MARVELD3 CCNB2 STK31 RAD51AP1 ZWINT FANCD2 CDC6 RRM2 MCM4 UCHL3 NUDCD1 ASPM S100A11 LIF SFXN4 GTSE1 MELK OVOL1 MKI67 KLK6 PABPC1L CDCA2 PRC1 GTPBP4 HOXA9 GAD1 GPSM2 NUSAP1 PROX1 MSX2 EZH2 TFAP2C ECT2 RACGAP1 S100A6 TPX2 KIF18B TFAP2A CXCL1 KRT18 BUB1 TIMM17A TOP2A CEP55 GINS4 BRCA1 LAPTM4B UHRF1 SKP2 NPM1 TRIM31 HOXC6 EIF3B ENO1 SPDL1 MCM5 AURKA MAD2L1 MYBL2 RAD18 PITPNB CHEK1 SKA3 CEP72 THOC3 KIF15 MCM2 SLC39A10 MYOF MTCH2 NEAT1 HMGA1 WDR72 CENPW PGRMC1 ITPA ARL5B MCM7 HSPE1 DCAF13 HSPH1 XRCC4 POLD3 CDCA5 RAD54B CKS1B HUS1 NCAPG SNRPD1 ESCO2 APEX2 JUP CDH3 EML4 MRPL13 ABHD10 ZNF367 BARD1 RANBP1 UPP1 BUB3 STK3 FEN1 WDR90 KCNE3 ATG16L1 CHI3L1 CDKN3 NMU ATAD2 FUBP1 SNRPB LRP8 PRR11 DPP3 SPP1 S100A10 BRIP1 PMEPA1 BIRC5 CKAP2 DSCC1 RRS1 SMC4 ZDHHC11 MRPS10 PTMAP4 CDK12 CDC20 CKS2 NCAPG2 CCNE1 CSTF3 FAM50A DLGAP5 PDZK1IP1 up
## WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP 0.0015699 0.0317567 0.5734851 2.540070 0 134 UNC5CL CD24 STK39 ELOVL6 GDA TOX3 TSPAN8 GALNT3 BZW2 KDELR2 PLS1 FRK LRRC8B SYT13 PERP GMDS OCIAD2 BRI3BP GALNT7 NET1 SYTL2 GFPT1 SFXN1 RASSF6 ABCC3 EPCAM KCNK1 CPD NME7 EDEM3 TPD52 GALNT4 GOLPH3 PDZD8 C3orf52 ESRP1 GNPNAT1 SEC24A COX7A2 ECT2 ASPHD2 MYO6 RASEF CASK GPR160 CHMP4C ABHD17C SH3RF1 ERBB3 SFN MAL2 DDAH1 ITGA6 ATP8B1 ELL3 TMEM30B ATP1B1 TSTA3 SLC35A3 ABCD3 SAR1B ARHGAP12 TMED4 PBLD NQO1 MAP7 MUC1 TNPO1 CTSE ARSD LLGL2 FNIP2 CA2 GPATCH4 ABHD2 ACBD5 TM9SF3 up
## WHITEFORD_PEDIATRIC_CANCER_MARKERS 0.0016103 0.0317567 0.5903122 2.522490 0 108 MND1 CDCA7 NME1 DHFR CDK4 PBK CDCA8 TTK UBE2T CENPF CDK1 NEK2 NUF2 PTTG1 CCNB1 KIF14 CENPA ILF2 PCNA PON3 CCNB2 TYMS ZWINT RRM2 MCM4 CDC25A MELK MKI67 CDCA2 PRC1 GAPDH ASF1B NUSAP1 GPX7 STMN1 TPX2 PAFAH1B3 NUDT1 BUB1 TOP2A PSAT1 SOX4 UHRF1 ESPL1 CCDC34 CDC45 ENO1 MCM5 AURKA RCC2 MAD2L1 MYBL2 KIF11 RFC4 POLQ up
## ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 0.0015480 0.0317567 0.5482005 2.516827 0 166 LEMD1 STYK1 SLC4A11 MYEOV CKMT1B KCNN4 DKK1 C1GALT1 RHBDL2 GPR87 SCIN PPP1R1B GCNT3 OLFM4 ITGA2 CEACAM5 FA2H GJB4 GALNT6 SOX21 TMPRSS4 TUFT1 FERMT1 BCL2L15 CDH17 SLC6A20 ANKRD22 VSTM2L SIX4 QPCT AP1S3 GPR35 REG4 BIK ANLN LGALS4 TTK KCNK1 CYP2S1 LAMC2 SERPINB5 CCNB2 CDX2 PTPRR C15orf48 KLK6 MYO1A APOBEC1 TPX2 ASPHD2 DTX2 BUB1 TOP2A CEP55 GPR160 HSH2D TRIM31 MUC17 KRT19 PPP1R14D AURKA TJP3 KIF11 TSPAN1 NFE2L3 KIF15 SFN GJB5 MYOM3 ELL3 GJB3 LIPH DAPP1 ST14 SERPINB2 CST6 LGALS3 PMAIP1 CDH3 CBLC LAMB3 TFCP2L1 IGFL2 CTSE KRT6B up
## BENPORATH_PROLIFERATION 0.0015649 0.0317567 0.5619711 2.502233 0 137 MND1 GGCT KDELR2 AVL9 SRPK1 CDCA7 PRIM2 NDC80 APOBEC3B EXO1 PBK ANLN TTK UBE2T CENPF CDK1 NEK2 NUF2 PTTG1 DAP3 TP53BP2 CENPM CENPA ILF2 PCNA DTL MAGOHB CCNB2 FAM3C TYMS RAD51AP1 RRM2 ASPM S100A11 C1orf112 PRC1 PDCD5 PARP1 GTPBP4 GPSM2 CDC123 EZH2 RACGAP1 STMN1 CTPS1 MSH2 BUB1 TOP2A CMC2 MRPL9 HSPA14 AURKA MAD2L1 SUV39H2 MCM3 MYBL2 RFC4 KNSTRN PPIL1 FAM49B GDI2 NFE2L3 MCM2 PRPF18 S100A9 PSMB4 CDCA5 CKS1B NCAPG SNRPD1 CDT1 SPAG5 LGALS8 RIT1 SNRPG RANBP1 PURB RAD54L CDKN3 ATAD2 LRP8 CNIH4 RBM8A PKMYT1 BIRC5 COX5A CKS2 IDH2 TMEM14A RAD51 CTSV GART PSMA3 CSNK1G1 PFDN2 CSE1L CSTB LBR PDCD10 DBF4 CMSS1 CHAF1B DCUN1D5 HDAC2 up
## CROONQUIST_IL6_DEPRIVATION_DN 0.0015823 0.0317567 0.6005625 2.496970 0 91 KNTC1 GINS1 APOBEC3B DHFR STIL TRIP13 FOXM1 HMMR BUB1B CDK1 PTTG1 CCNB1 KIF14 FANCI CENPA PCNA CCNB2 TYMS ZWINT CDC6 RRM2 MCM4 CDC25A MKI67 GMPS CCNE2 STMN1 TPX2 FRZB BUB1 TOP2A BRCA1 SKP2 GALE CDC45 AURKB PLK1 AURKA MAD2L1 MCM3 MYBL2 KIFC1 KIF11 CHEK1 MCM2 HMGA1 MCM7 KIF22 CKS1B KIF2C TRAIP CCNF POLE2 SPAG5 PTP4A3 CDKN3 SPC25 PLK4 SEPHS1 SPP1 CHAF1A SMC4 CDC20 CKS2 up
## NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON 0.0016556 0.0317567 0.6951402 2.494891 0 42 TSPAN8 CPSF6 IL26 METTL1 CCT2 YEATS4 NUP107 MDM1 C12orf66 RAB3IP IL22 CDK4 AVIL CAND1 MDM2 FRS2 CNOT2 TSFM C12orf56 SLC35E3 PTPRR RAP1B XPOT TSPAN31 BEST3 LGR5 IFNG DYRK2 TBK1 CTDSP2 ZFC3H1 CYP27B1 OS9 up
## UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN 0.0023981 0.0317567 -0.6757572 -2.488350 0 34 CITED2 SIK1 NR4A1 EGR1 KLF4 HBEGF GEM ZFP36 BMP2 KLF2 DUSP1 HLX ATF3 NR4A2 PDK4 MAP3K8 RCAN1 MCL1 NEDD9 down
## ZHAN_MULTIPLE_MYELOMA_PR_UP 0.0016892 0.0317567 0.6938579 2.464735 0 41 MCM10 DEPDC1B TRIP13 FOXM1 BUB1B TTK UBE2T CDK1 E2F8 NEK2 NUF2 CCNB1 KIF14 CENPL FANCI CCNB2 TYMS RRM2 ASPM PRC1 NUSAP1 EZH2 RACGAP1 MPC2 TPX2 TOP2A CCDC34 AURKA RFC4 up
## SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 0.0013850 0.0317567 0.4822437 2.458950 0 426 SLC9A2 PKP2 ELOVL6 UGT8 KIF2A HELLS YEATS4 MCM10 KNTC1 PRIM2 NDC80 SRD5A1 NME1 GINS1 KIF20A TFG HJURP APOBEC3B TROAP DNA2 EXO1 TRIP13 FOXM1 HMMR PBK BUB1B ACP1 CDCA8 TTK CCT5 CENPF CDK1 SFXN1 E2F8 WDHD1 NEK2 SLC38A1 PTTG1 CCNB1 LDHB DEPDC1 PARPBP CENPM KIF14 FANCI LMNB1 CENPA PCNA MUC16 DTL MAGOHB WDR43 TBRG4 CCNB2 TYMS RAD51AP1 ZWINT AP2B1 CDC6 RRM2 PAICS MCM4 TWF1 CDC25A SMC6 ASPM AGMAT DNM1L GTSE1 MELK MKI67 PRKDC PRC1 GAPDH GPSM2 NUSAP1 CCNE2 FOXG1 EZH2 RACGAP1 IGF2BP3 STMN1 TPX2 KIF18B YKT6 BUB1 ORC1 LRIF1 PRPS1 NETO2 TOP2A CEP55 GINS4 WDYHV1 PSAT1 CDC25C LRPPRC FBXO5 CMAS CDK5R1 PKM CD70 TTF2 CMC2 CDC45 VANGL1 AURKB AGPAT5 KIF23 MCM5 AURKA MAD2L1 SSX2IP MYBL2 AK4 KIF11 RFC4 CENPQ CHEK1 MTHFD2 KLRC1 IL1RAP KIF15 KAZALD1 XPNPEP1 MTCH2 PRIM1 PSMA5 HMGA1 FGFR1OP TPRKB FKBP4 SEMA3A DNAJC9 CDC7 HCCS MTIF2 NABP2 MSH6 NCAPG NCAPD2 DGUOK KIF2C PNP SLC25A10 CDT1 POLE2 PMAIP1 PSME3 SPAG5 UBE2V2 PAX8 MRPL13 NDUFA9 PTBP3 YEATS2 EIF5B RBL1 CENPI BUB3 NOLC1 PSMB2 WDR76 MPHOSPH9 ZWILCH RAD54L GNAI3 MTF2 TSR1 GPD2 UBA6 CDKN3 SPC25 R3HDM1 STC2 QSER1 PFN2 RAB22A SLC2A1 NMU ATAD2 SNRPB PLK4 ZNF248 YME1L1 GPR19 SEPHS1 ERCC6L CAD BRIP1 PARL RAN BIRC5 GOLT1B CKAP2 GPR37 TUBG1 EGLN3 TUBA4B EXOSC2 GABPB1 PA2G4 CDC20 CKS2 NCAPG2 NCAPD3 PPID CCNE1 DLGAP5 CHRNA5 SLC7A5 MCM6 HAT1 NUP62 up
## DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP 0.0014599 0.0317567 0.4953288 2.456038 0 305 DEPTOR E2F7 KCNK5 HELLS MCM8 MCM10 KNTC1 CDCA7 NUP107 PCP4 BLM DEPDC1B SLC27A2 FAM111B NME1 GINS1 FIGNL1 BRI3BP TROAP STIL PAQR4 DNA2 EXO1 TRIP13 FOXM1 PBK LYPD6 BUB1B ANLN TTK UBE2T CDK1 E2F8 GLB1L2 WDHD1 RBBP8 PTTG1 POLD2 RPA3 CENPM CENPL FANCI LMNB1 GMNN PCNA DTL IQGAP3 CCNB2 C1QTNF6 TYMS SYTL5 ZWINT FANCD2 CDC6 RRM2 E2F2 MCM4 ASPM CDCA7L NOS1AP CLSPN DHTKD1 GTSE1 MELK MKI67 CDCA2 PRC1 ASF1B NUSAP1 CCNE2 SLC39A6 TICRR RACGAP1 STMN1 TPX2 TCF19 PKIB BUB1 NR2C2AP XYLB SNRNP25 TOP2A CEP55 BRCA1 UHRF1 FBXO5 SKP2 ESPL1 TTF2 TFF1 CCDC34 CDC45 AURKB SPDL1 KIF23 PLK1 MCM5 AURKA MIS18A MANEAL SUV39H2 MCM3 MYBL2 KIFC1 RAD18 KIF11 RFC4 KNSTRN CHEK1 SKA3 POLQ IL1RAP MCM2 MMS22L PRIM1 MTHFD1 SLC26A2 POLA2 TIMELESS MCM7 FKBP4 CEP85 POLD3 RMI1 CDCA5 RAD54B HAUS4 XRCC2 NCAPG NCAPD2 ESCO2 KIF2C TRAIP CDT1 POLE2 SPAG5 ZNF367 BARD1 UNG RBL1 CENPI HAUS8 WDR76 RNASEH2A FEN1 MPHOSPH9 ZWILCH L2HGDH RAD54L CDK2 SPC24 XBP1 STC2 DCLRE1B SLC2A1 ATAD2 MYO19 PLK4 PRR11 ABHD2 BRIP1 CHAF1A PKMYT1 BIRC5 DSCC1 NFATC2 EXOSC2 TMED8 NCAPG2 NCAPD3 DLGAP5 RRM1 CHRNA5 SLC7A5 MCM6 POLE up
## KANG_DOXORUBICIN_RESISTANCE_UP 0.0016474 0.0317567 0.6553348 2.446491 0 51 GINS1 HJURP FOXM1 HMMR PBK BUB1B CDCA8 CDK1 CENPM FANCI LMNB1 CENPA TYMS RAD51AP1 ZWINT CDC6 RRM2 MCM4 ASPM MKI67 PRC1 ASF1B NUSAP1 TPX2 BUB1 TOP2A PLK1 AURKA MAD2L1 RFC4 POLQ POLA2 NCAPG NQO1 BARD1 CDKN3 ATAD2 PLK4 BIRC5 DSCC1 CDC20 NCAPG2 RRM1 up
## LEE_EARLY_T_LYMPHOCYTE_UP 0.0015873 0.0317567 0.5794216 2.423248 0 95 E2F7 MCM10 NDC80 GINS1 KIF20A CEP70 TNFRSF21 GALNT7 HMMR PBK BUB1B TTK UBE2T CDK1 E2F8 NEK2 NUF2 PTTG1 CCNB1 KIF14 FANCI PON1 CENPA DTL CCNB2 TYMS RAD51AP1 RRM2 E2F2 MCM4 TSHR CDC25A ASPM FAIM MELK MKI67 CDCA2 PRC1 NUSAP1 KIF18B BUB1 TOP2A CEP55 UHRF1 AURKA KIF11 KIF15 MCM2 CENPW NCAPG KIF2C RAPGEF5 SLC1A4 SCRN1 CEP128 CDKN3 ATAD2 PRR11 BIRC5 DSCC1 MZB1 CKS2 CXXC5 DLGAP5 up
## CROONQUIST_NRAS_SIGNALING_DN 0.0016181 0.0317567 0.6102278 2.421596 0 68 NDC80 GINS1 APOBEC3B CHEK2 STIL TRIP13 FOXM1 BUB1B CDK1 PTTG1 CCNB1 CENPA PCNA CCNB2 ZWINT CDC6 MCM4 MKI67 STMN1 TPX2 TOP2A CDC25C GALE AURKB PLK1 AURKA MCM3 MYBL2 KIF11 CHEK1 MCM2 HMGA1 MCM7 POLD3 KIF22 CKS1B KIF2C TRAIP SPAG5 PTP4A3 CDKN3 SPC25 PLK4 CHAF1A SMC4 CDC20 RAD51C up
## SONG_TARGETS_OF_IE86_CMV_PROTEIN 0.0016639 0.0317567 0.6444075 2.413731 0 52 BLM DHFR FOXM1 CDK1 PTTG1 FLAD1 PCNA TYMS ZWINT DLEU1 UMPS EZH2 TPX2 TOPBP1 MSH2 TMEM106C MCM5 MAD2L1 MCM3 MYBL2 KIF11 MCM2 RAB27A MCM7 DNAJC9 POLD3 CASP3 PNP CDT1 BARD1 RPA1 UNG PPIH RAD51C CCNE1 RRM1 MCM6 up
## RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP 0.0013263 0.0317567 0.4606546 2.407135 0 588 RALGPS2 ELOVL6 CLDN1 KIF2A COA1 LACTB2 HELLS GGCT OSBPL3 MCM8 KNTC1 CDCA7 GPT2 PHF14 NNT ATIC SRD5A1 UTP15 NME1 PRTFDC1 DPY19L1 GINS1 NLN NUP155 BRIX1 DHFR FIGNL1 DENND5B STIL TTC26 PBK BUB1B ANLN ACP1 HPS3 TTK CBX3 CENPF HEATR1 GFPT1 CDK1 SFXN1 WDHD1 MRPS9 RBBP8 CCT6A CCNB1 POLD2 PARPBP UCK2 C5orf22 ENC1 KIF14 CKLF WDR3 FANCI LMNB1 RBAK TIMM23 PCNA TPR ATR DTL SNAPC1 GFM2 IFI16 IQGAP3 GLRX3 TYMS RAD51AP1 ZWINT ERCC8 FANCD2 CDC6 TIPRL PAICS MCM4 TIPIN TWF1 NDC1 AFF4 HLTF GEN1 SMC6 FBXO22 OSMR DNAJC10 DNM1L NOP58 PMS1 C15orf48 CPSF3 GTSE1 MKI67 MIPOL1 PRKDC GMPS PRC1 SSBP1 RAI14 PDCD5 RBBP4 GTPBP4 WDR12 GPSM2 NUSAP1 CCNE2 CDC123 PRKAA1 TMEM161B GNL2 ZNF146 ECT2 RACGAP1 DHX9 IGF2BP3 STMN1 CTPS1 TOPBP1 CCDC14 YKT6 C5orf34 TIMM17A PSPH HSPA9 LRIF1 NETO2 LARP1B TMEM45A BRCA1 E2F5 PSAT1 CSNK1A1 LRPPRC LAPTM4B MFN1 RSRC1 FBXO5 SUB1 GALE NPM1 RPE TSEN15 TTF2 CCDC34 CMC2 KBTBD2 HSPA14 ENO1 AGPAT5 SPDL1 SLC4A7 AURKA MIS18A SSR3 ORC6 MAD2L1 SSX2IP SUV39H2 AK4 RAD18 RFC4 CENPQ CHEK1 MTHFD2 GDI2 CCT8 TMEM167A IL1RAP RHOBTB3 MCM2 FKBP14 LEO1 INTS7 PSMA5 TSN CENPW STEAP3 SOAT1 ARL5B MCM7 DCAF13 MAD2L2 KISS1R ABCD3 XRCC4 MPHOSPH10 SAR1B DNAJC9 HCCS GTPBP10 MTIF2 MICU1 CKS1B MSH6 NCAPG ASAH2 EIF2S3 PNPT1 HSPD1 SNRPD1 LIN9 KIF2C CCDC77 PNP SLC30A5 PMAIP1 UBE2V2 HSPA4 MRPL47 NQO1 MRPL13 ABCE1 CHCHD3 IDE C1orf43 EIF5B ZNF367 RCC1 TPGS2 UPP1 RBL1 BUB3 NOLC1 SNX13 PHGDH ME2 WDR76 RNASEH2A SOCS4 FEN1 EIF2S2 ADAM9 SEC61A2 ZC3H15 ZWILCH SLC39A9 KIF20B PRPF40A AGGF1 CANX NABP1 HOXB7 SUPT16H RPAP3 GNAI3 MTFR1 GPD2 UBA6 RFWD3 EIF2S1 STC2 MANEA DERL1 ATP1B3 SLC2A1 ATAD2 MTFP1 DYNC2H1 PRR11 YME1L1 MRPL37 AP1AR BCCIP COPS8 GSR YWHAZ RAN CKAP2 ORC5 TUBG1 TRUB1 SMC4 CHAC2 RAD51C GPX8 CKS2 CCNE1 DLGAP5 CALU RRM1 CHRNA5 CBFB MCM6 FH HAT1 KIAA0586 PXDN NAA15 SLC25A32 MRPS12 KLHL7 CEBPZ PPAT ZBTB8OS GART PSMA3 LINC00662 FAF1 HSPA4L C4orf46 UCHL5 VKORC1L1 CRNDE NPM3 SEH1L CSE1L TFDP2 UBE2S PSMD8 CYCS ITCH TNFRSF10B SASS6 SMC2 DCUN1D4 U2SURP CCNA2 up
## CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP 0.0015552 0.0317567 0.5248020 2.403973 0 164 CD24 SOX9 FDCSP HELLS CENPK FLVCR1 SEL1L3 CDCA7 NDC80 DEPDC1B FUNDC1 KIF20A HJURP TNFRSF21 GALNT7 TRIP13 FOXM1 PBK BACE2 BUB1B ANLN TTK CENPF CDK1 E2F8 NEK2 TRNP1 SLC38A1 NUF2 PTTG1 CCNB1 DEPDC1 KIF14 FANCI LMNB1 DTL CCNB2 RAD51AP1 PDE9A ZWINT CDC6 ASPM CDCA7L MKI67 PRC1 TMED3 NUSAP1 MARCKSL1 EZH2 ECT2 RACGAP1 IGF2BP3 TPX2 PAFAH1B3 KIF18B TOP2A CEP55 SOX4 COLCA2 FBXO5 PKM TTF2 AURKB KIF23 AURKA ORC6 MAD2L1 CKAP2L KIF11 RFC4 UGCG MCM2 SLC39A10 RMI2 ETV4 LDLRAD3 CDC7 CDCA5 KIF2C NT5DC2 BARD1 B4GALT5 ELOVL7 FEN1 DBN1 PTP4A3 CDKN3 TMEM51 PRR11 TMEM65 ASRGL1 PM20D2 BIRC5 DSCC1 SMC4 up
## INAMURA_LUNG_CANCER_SCC_DN 0.0022026 0.0317567 -0.8476702 -2.397832 0 13 ADARB1 RASL12 CAV1 ADAMTS8 PHACTR2 ADAMTSL3 VWF ST6GALNAC5 NR2F2 MCL1 ABCA8 PGM5 down
## VILLANUEVA_LIVER_CANCER_KRT19_UP 0.0015480 0.0317567 0.5243342 2.395095 0 160 SOX9 C2CD4A ARX DROSHA MCM8 MCM10 KNTC1 GABRB3 METTL9 BLM NDC80 USP37 DEPDC1B GINS1 KIF20A HJURP TROAP STIL DNA2 ANLN CDCA8 TTK STRBP PTTG1 TRMT6 CENPM FANCI LMNB1 OLA1 TAC1 ZWINT PDZD8 CDC25A DNM1L CASP2 MELK MKI67 GPSM2 FMO9P COL22A1 EZH2 GAL3ST1 ECT2 STMN1 TPX2 DDX4 BUB1 TOP2A CEP55 SOX4 DCLRE1C KIF23 ZNF354A CKAP2L UPF3B KIF15 PNMA3 SUMO2 MEX3C POLD3 CDC7 NCAPG KIF2C AP1G2 BARD1 KIF20B RAD54L ZBED5 GPD2 SLC35D3 TUG1 DCLRE1B FUBP1 PLK4 RAB13 ZNF678 IFT57 CEP290 TDG CDC20 DLGAP5 RRM1 MCM6 NR6A1 SIPA1L3 up
## CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP 0.0027100 0.0317567 -0.5411641 -2.393873 0 94 CSDC2 TCAP NES JUN PER1 TMEM204 SYNPO2L CNN1 MFAP4 RGCC DIXDC1 ZFP36 CEBPD FHL1 KLF2 IRS2 PIK3R1 FLNC FSTL3 ANKRD2 PLA2G5 TIMP3 ATF3 CYP4B1 NFKBIA PDK4 METTL7A ZFAND5 KLF9 MCL1 NCKIPSD CEBPB FOXO3 BTG2 MT2A ZBTB16 CALD1 TIPARP AGTR1 CLU CDC37L1 DNAJB5 TSC22D3 IER5 VCL CD163 MT1E down
## REACTOME_NGF_STIMULATED_TRANSCRIPTION 0.0024814 0.0317567 -0.6273377 -2.390700 0 39 ARC JUND EGR2 ID4 EGR1 FOSB ASCL1 ID3 FOS SH3GL3 JUNB LYL1 ID2 SRF ID1 VGF TRIB1 ATF1 down
## LANDIS_BREAST_CANCER_PROGRESSION_DN 0.0026042 0.0317567 -0.5623246 -2.383663 0 68 PENK GAS6 CLEC3B QKI KLF4 THBD AHNAK ALAS1 MAP4 FZD4 DPT SULT1A1 PPP2R5A VWF EPHX2 MAN1A1 ZEB1 MFNG GHR HSPB8 ANGPTL2 ACAA1 SORBS1 PGM1 down
## KONG_E2F3_TARGETS 0.0015823 0.0317567 0.5741706 2.379219 0 88 E2F3 CENPH CENPK KIF20A HJURP FIGNL1 DNA2 HMMR PBK BUB1B UBE2T CENPF RBBP8 NUF2 CCNB1 DEPDC1 LMNB1 IQGAP3 RPRD1B TYMS RAD51AP1 CDC6 MELK MKI67 PRC1 ASF1B IGF2BP1 NUSAP1 EZH2 RACGAP1 TPX2 BUB1 TOP2A BRCA1 SKP2 SPDL1 PLK1 AURKA MCM3 KIF11 CENPQ FBXO45 MED1 PRIM1 CDC7 CDCA5 NCAPG NCAPD2 KIF2C CCNF RBL1 FEN1 RAD54L SPC25 ERCC6L TAF1D CDC20 NCAPG2 CCNE1 DLGAP5 up
## WINNEPENNINCKX_MELANOMA_METASTASIS_UP 0.0015625 0.0317567 0.5245879 2.377122 0 150 RHBDL2 KDELR2 KNTC1 PRIM2 PHF14 NDC80 NME1 ZNF587 DHFR EXO1 ANLN CDCA8 UBE2T CCT5 CENPF CDK1 NEK2 NUF2 PTTG1 CCNB1 RPA3 PARPBP DCBLD2 OLA1 CENPA GMNN PCNA CCNB2 TYMS ZWINT CDC6 RRM2 PAICS MCM4 NUDCD1 ASPM RBMX MELK GEMIN6 GMPS PRC1 ECT2 RACGAP1 PWP1 CCT4 KIF18B BUB1 TOP2A CEP55 RSRC1 UHRF1 CDC45 AURKA SSR3 KIF11 RFC4 KNSTRN CHEK1 FAM98A ARF4 TIMELESS CDCA5 CKS1B MSH6 NCAPG HSPD1 KIF2C SPAG5 HSPA4 SNRPG ZNF367 RANBP1 ENY2 UBFD1 RAD54L CDKN3 SPC25 CCT7 ATAD2 BIRC5 DSCC1 EEPD1 MRPS10 CKS2 NCAPG2 XPO1 DLGAP5 MCM6 CHTOP up
fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='CANARY: G vs P')##
##
## |pathway | pval| padj| ES| NES| nMoreExtreme| size|leadingEdge |state |
## |:-------|----:|----:|--:|---:|------------:|----:|:-----------|:-----|
fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## ------------ ---------- ---------- ---------- --------- ------------- ----- ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------
## GNF2_BUB1B 0.0016694 0.0161448 0.7366708 2.746961 0 49 HELLS NDC80 GINS1 KIF20A HJURP HMMR BUB1B CDCA8 TTK CENPM KIF14 FANCI LMNB1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 PAICS MCM4 ASPM MELK ASF1B RACGAP1 BUB1 TOP2A CEP55 ESPL1 AURKB NUP205 PLK1 AURKA MCM3 KIF11 MCM2 up
## GNF2_MCM4 0.0016863 0.0161448 0.7247994 2.714081 0 52 HELLS NDC80 GINS1 FOXM1 HMMR BUB1B CDCA8 TTK CENPM KIF14 FANCI LMNB1 GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT RRM2 PAICS MCM4 ASPM MELK ASF1B RACGAP1 KIF18B BUB1 TOP2A ESPL1 AURKB MCM5 AURKA MAD2L1 MCM3 KIF11 RFC4 MCM2 MCM7 up
## GNF2_CCNA2 0.0015748 0.0161448 0.6827607 2.695895 0 65 NDC80 KIF20A HJURP FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 KIF14 FANCI CENPA GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 ASF1B NUSAP1 EZH2 RACGAP1 TPX2 KIF18B TOP2A ESPL1 AURKB PLK1 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MCM7 CKS1B NCAPG NCAPD2 up
## MODULE_54 0.0014793 0.0161448 0.5548097 2.653734 0 241 ELOVL6 PLAT ITGA2 SRPK1 KNTC1 CDCA7 DDX11 BLM NDC80 DEPDC1B TM4SF1 NME1 GINS1 HJURP APOBEC3B SNRPE DHFR TROAP TRIP13 CDK4 FOXM1 HMMR PBK BUB1B ANLN TTK UBE2T CCT5 CENPF CDK1 E2F8 CDH1 NEK2 NUF2 CCT6A PTTG1 CCNB1 RPA3 DEPDC1 RHNO1 KIF14 LMNB1 EFHC2 CENPA GMNN PCNA CCNB2 TYMS ZWINT CDC6 RRM2 MCM4 NRIP3 ASPM MELK MKI67 GAD1 ASF1B GPSM2 NUSAP1 CCNE2 MB DLEU1 ECT2 AIMP2 CTPS1 TPX2 TOPBP1 NUDT1 MSH2 BUB1 HOXC10 PSPH ORC1 BEST3 TOP2A CEP55 CDC25C LAPTM4B TMEM106C PRDX4 CDC45 AURKB AGPAT5 KIF23 PLK1 MCM5 ZNF267 AURKA MAD2L1 MCM3 MYBL2 KIFC1 KIF11 RFC4 KNSTRN CHEK1 ARL6IP1 TRIM24 MTHFD2 POLQ PHF5A MCM2 PRIM1 HMGA1 TSN TIMELESS MCM7 HSPH1 SCG5 CDC7 CDCA5 CKS1B NCAPD2 KIF2C PNP CCNF POLE2 APEX2 PMAIP1 SPAG5 NQO1 SQLE MID1 LRRC17 NT5DC2 RCC1 BARD1 UNG RANBP1 SNRPC FEN1 ZWILCH RAD54L CDKN3 ATAD2 SNRPB LRP8 CNIH4 PLK4 PRR11 AHCY CHAF1A PKMYT1 BIRC5 CKAP2 SMC4 AMPH CDC20 MUCL1 CKS2 DLGAP5 RRM1 SLC7A5 MCM6 up
## GNF2_RRM2 0.0016978 0.0161448 0.7454536 2.633917 0 39 NDC80 FOXM1 HMMR BUB1B CDCA8 CENPF CDK1 CENPM LMNB1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 NUSAP1 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA MCM3 KIF11 MCM2 up
## GNF2_RRM1 0.0015456 0.0161448 0.6221144 2.601868 0 86 NDC80 GINS1 DHFR FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 CCT6A CENPM KIF14 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT RRM2 PAICS MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 KIF18B MSH2 TOP2A AURKB MCM5 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MRPL35 MCM7 SNRPD1 CHCHD3 SNRPG FEN1 EIF2S1 PLK4 PCCB RAN BIRC5 SMC4 PA2G4 CDC20 CKS2 DLGAP5 RRM1 MCM6 FH HAT1 HNRNPAB SERBP1 ANP32E SMC2 CCNA2 up
## GNF2_PCNA 0.0015748 0.0161448 0.6584105 2.599747 0 65 NDC80 GINS1 FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 TPX2 KIF18B MSH2 TOP2A ESPL1 MCM5 AURKA MCM3 MYBL2 KIF11 RFC4 KIF15 MCM2 PRIM1 MCM7 DNAJC9 POLE2 FEN1 RAD54L PAXIP1 PLK4 BIRC5 SMC4 PA2G4 CDC20 CKS2 DLGAP5 RRM1 MCM6 HNRNPAB up
## GNF2_HMMR 0.0016779 0.0161448 0.6926553 2.559051 0 46 NDC80 KIF20A FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA KIF11 MCM2 up
## GNF2_RFC4 0.0016502 0.0161448 0.6598827 2.522490 0 57 CCT2 MCM10 KNTC1 NDC80 GINS1 SNRPE FOXM1 TTK CENPF CDK1 RPA3 FANCI GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT PAICS MCM4 ASPM CTPS1 MSH2 TOP2A MCM3 KIF11 RFC4 MCM2 PRIM1 TIMELESS MCM7 CKS1B MSH6 NCAPD2 SNRPD1 RANBP1 FEN1 SUPT16H RAD54L PLK4 RAN BIRC5 SMC4 CKS2 RRM1 MCM6 up
## GNF2_CDC2 0.0016340 0.0161448 0.6533356 2.521161 0 59 NDC80 KIF20A HJURP FOXM1 HMMR CDCA8 TTK CENPF CDK1 E2F8 PTTG1 FANCI PCNA CCNB2 TYMS ZWINT RRM2 ASPM MELK MKI67 PRC1 NUSAP1 EZH2 TPX2 KIF18B TOP2A AURKA MYBL2 KIFC1 KIF11 RFC4 KIF15 MCM2 PRIM1 DNAJC9 NCAPG CCNF FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 up
## GNF2_SMC4L1 0.0015873 0.0161448 0.6129553 2.505897 0 80 NDC80 GINS1 DHFR FOXM1 HMMR BUB1B CDCA8 TTK CBX3 CENPF CDK1 E2F8 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT MCM4 ASPM PRC1 NUSAP1 SRSF1 RACGAP1 KIF18B MSH2 TOP2A FBXO5 MCM5 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MRPL35 MCM7 DNAJC9 SNRPD1 POLE2 SNRPG FEN1 ZWILCH SUPT16H EIF2S1 GAR1 PLK4 PCCB CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 HAT1 HNRNPAB SERBP1 ANP32E SMC2 CCNA2 up
## GNF2_PA2G4 0.0015649 0.0161448 0.6151580 2.499555 0 75 LSM5 CCT2 NUP107 NDC80 MRPL15 SNRPE XRCC5 CDK4 BUB1B CCT5 CCT6A CCT3 CENPM OLA1 GMNN PCNA PAICS MCM4 MRPL3 MELK ETFA GMPS SSBP1 CCT4 LRPPRC MCM5 MCM3 NAE1 MTHFD2 PSMD11 METTL5 MRPL35 MCM7 CKS1B SNRPA SNRPD1 ABCE1 CHCHD3 SNRPG RANBP1 BUB3 MRPL22 EIF2S1 SNRPB CAD RAN PSMA4 PA2G4 RRM1 FH HAT1 NDUFS1 NCL PSMA3 HNRNPA2B1 SERBP1 CSE1L up
## GNF2_CENPF 0.0016313 0.0161448 0.6476011 2.486812 0 58 MCM10 NDC80 HJURP FOXM1 HMMR CDCA8 TTK CENPF CDK1 E2F8 PTTG1 FANCI PCNA CCNB2 TYMS ZWINT RRM2 ASPM MKI67 PRC1 NUSAP1 TPX2 KIF18B TOP2A AURKA MCM3 MYBL2 KIFC1 KIF11 RFC4 KIF15 MCM2 PRIM1 MCM7 DNAJC9 CCNF FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 HAT1 up
## GNF2_CDC20 0.0016920 0.0161448 0.6604844 2.474546 0 53 NDC80 KIF20A FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 PTTG1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 TPX2 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA KIF11 MCM2 CKS1B KIF2C SPAG5 PLK4 RAN BIRC5 SMC4 CDC20 CKS2 DLGAP5 RRM1 up
## GNF2_ESPL1 0.0017036 0.0161448 0.7150924 2.463234 0 35 KIF20A FOXM1 HMMR BUB1B CDCA8 CENPM CENPA PCNA CCNB2 RRM2 PAICS MCM4 ASPM MELK MKI67 ASF1B TPX2 BUB1 TOP2A ESPL1 AURKB PLK1 MAD2L1 KIF11 CKS1B NCAPD2 KIF2C SPAG5 up
## GNF2_CCNB2 0.0016694 0.0161448 0.6525990 2.457845 0 54 NDC80 KIF20A FOXM1 HMMR PBK BUB1B CDCA8 TTK CENPF CDK1 PTTG1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK PRC1 NUSAP1 RACGAP1 TPX2 KIF18B BUB1 TOP2A ESPL1 AURKA KIF11 RFC4 MCM2 KIF2C SPAG5 FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 up
## GNF2_FEN1 0.0016694 0.0161448 0.6492503 2.445233 0 54 NDC80 GINS1 DHFR FOXM1 HMMR TTK CENPF CDK1 E2F8 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT MCM4 PRC1 NUSAP1 RACGAP1 KIF18B MSH2 TOP2A MCM5 MCM3 KIF11 RFC4 MCM2 MCM7 DNAJC9 SNRPD1 POLE2 FEN1 GAR1 PLK4 PCCB SMC4 CKS2 DLGAP5 RRM1 HAT1 HNRNPAB up
## GNF2_TTK 0.0016920 0.0161448 0.6946281 2.441217 0 38 CCT2 NDC80 HJURP FOXM1 HMMR BUB1B TTK CENPF CDK1 FANCI GMNN PCNA CCNB2 TYMS ZWINT MCM4 ASPM MELK PRC1 NUSAP1 RACGAP1 TPX2 KIF18B TOP2A KIF11 RFC4 MCM2 up
## GNF2_RAN 0.0015898 0.0161448 0.5950974 2.429160 0 79 CCT2 ATIC NME1 KIF20A MRPL15 SNRPE XRCC5 CCT5 CCT6A CCT3 RPA3 OLA1 PAICS MRPL3 EMG1 MELK ETFA PRKDC GMPS SSBP1 CTPS1 CCT4 HSPA9 LRPPRC MCM3 RFC4 NAE1 GNL3 MTHFD2 CCT8 PSMA5 MRPL35 CKS1B SNRPA MSH6 NCAPD2 SNRPD1 SNRPD2 ABCE1 SNRPG RANBP1 BUB3 SNRPC EIF2S2 MRPL22 EIF2S1 HNRNPC CCT7 POLR2H MRPS33 RAN PSMA4 PA2G4 CDC20 RRM1 PSMA3 HNRNPA2B1 SERBP1 CSE1L up
## GNF2_CKS2 0.0016694 0.0161448 0.6511093 2.414489 0 48 CCT2 NDC80 GINS1 KIF20A FOXM1 HMMR TTK CENPF CDK1 PTTG1 RPA3 FANCI GMNN PCNA DTL CCNB2 TYMS ZWINT MCM4 ASPM PRC1 NUSAP1 RACGAP1 TOP2A RFC4 MCM2 MRPL35 SNRPD1 FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 HNRNPAB up
## GNF2_CKS1B 0.0016920 0.0161448 0.6781563 2.354375 0 36 NDC80 ATIC KIF20A TRIP13 CDCA8 RPA3 PAICS ASPM MELK GMPS ASF1B TPX2 CCT4 BUB1 ESPL1 AURKB MCM3 KIF11 RFC4 MRPL35 CKS1B NCAPD2 KIF2C RANBP1 RNASEH2A RAN BIRC5 PA2G4 CDC20 MCM6 up
## MODULE_125 0.0016863 0.0161448 0.6381411 2.299802 0 42 TERT PRIM2 DDX11 BLM CENPF POLD2 RPA3 GMNN PCNA RRM2 S100A11 SSBP1 RBBP4 TOPBP1 ORC1 TOP2A CDC45 MCM3 RFC4 PRIM1 CDC7 POLE2 RPA1 RNASEH2A FEN1 CDK2 CHAF1A RRM1 MCM6 POLE up
## MORF_UNG 0.0015949 0.0161448 0.5834362 2.291002 0 64 CCT2 ATIC PDCD6 CDK4 CCT5 COPS5 CCT3 VDAC1 PCNA CDC23 MRPL3 MAGOH SSBP1 SRSF1 AIMP2 MSH2 HSPA9 TMEM106C EIF3B DOCK3 RFC4 NHP2 MTHFD1 ALG8 AHSA1 HSPE1 NDUFAB1 HCCS RPA1 UNG POLE3 POLR2I PSMB2 DDX1 FEN1 up
## GNF2_CENPE 0.0016920 0.0161448 0.6490203 2.280932 0 38 NDC80 FOXM1 HMMR CDCA8 CENPF CDK1 PCNA CCNB2 TYMS ZWINT RRM2 ASPM MKI67 PRC1 NUSAP1 KIF18B BUB1 ESPL1 AURKB AURKA MYBL2 KIF11 PRIM1 CKS1B CCNF BIRC5 CDC20 CKS2 DLGAP5 RRM1 up
## MORF_RFC4 0.0015432 0.0161448 0.5121962 2.276880 0 130 SRPK1 LYPLA1 NDC80 ZNF131 TRIP13 TCEA1 HMMR BUB1B ACTL6A CCT5 GTF2A2 VDAC1 GPN1 KIF14 ILF2 TYMS ZWINT PRKDC XPOT SSBP1 MRPS27 SRSF1 HNRNPR PMEL CCT4 MSH2 BUB1 TOP2A LRPPRC ESPL1 SDHA SHMT2 MCM3 DOCK3 RFC4 NAE1 MCM2 PRPS2 HSPE1 DNAJC9 HCCS NDUFB3 SNRPA ALG3 DGUOK SPAG5 GOT2 AKR7A2 TGDS RPA1 UNG BUB3 PSMB2 MTX2 EIF2S2 RAD54L R3HDM1 CAD CHAF1A DNAJC11 POM121 XPO1 RRM1 MCM6 FH HAT1 CEBPZ HNRNPAB DDX18 HNRNPA2B1 MLEC UBE2S CYCS SERP1 CCNA2 PPM1G HDAC2 SSRP1 RUVBL2 EI24 KHDRBS1 PTGES3 up
## GNF2_MKI67 0.0016920 0.0161448 0.6999009 2.274556 0 28 KIF20A FOXM1 HMMR CENPF CDK1 CENPA PCNA ZWINT RRM2 ASPM MELK MKI67 NUSAP1 TPX2 KIF18B TOP2A ESPL1 AURKA KIF11 NCAPG NCAPD2 up
## GNF2_RFC3 0.0016978 0.0161448 0.6433066 2.273000 0 39 NDC80 FOXM1 HMMR CDK1 RPA3 FANCI RAD51AP1 PAICS MCM4 ASPM CTPS1 TOP2A MCM3 KIF11 RFC4 MRPL35 TIMELESS CKS1B MSH6 NCAPD2 SNRPD1 RANBP1 SUPT16H RAN BIRC5 SMC4 CKS2 RRM1 MCM6 SMC2 CCNA2 ADSL SSRP1 up
## GNF2_BUB1 0.0017123 0.0161448 0.7176513 2.272248 0 26 NDC80 KIF20A FOXM1 HMMR BUB1B CDCA8 GMNN CCNB2 RRM2 MCM4 ASPM MELK ASF1B BUB1 ESPL1 AURKB PLK1 CKS1B KIF2C CDT1 SPAG5 RANBP1 up
## GNF2_NS 0.0016835 0.0161448 0.6473302 2.269483 0 37 ATIC SNRPE CCT3 OLA1 PAICS MRPL3 GLO1 PRKDC SSBP1 PARP1 GTPBP4 MRPS27 CCT4 HSPA9 LRPPRC NPM1 GNL3 MTHFD2 CCT8 PSMA5 MSH6 SNRPD2 ABCE1 CCNG1 MRPS33 RAN PSMA4 TAF1D PSMA3 HNRNPA2B1 up
## MODULE_158 0.0016949 0.0161448 0.6354061 2.268399 0 41 TERT PRIM2 DDX11 BLM CENPF POLD2 RPA3 GMNN PCNA RRM2 S100A11 SSBP1 RBBP4 TOPBP1 ORC1 TOP2A CDC45 MCM3 RFC4 PRIM1 CDC7 POLE2 RPA1 RNASEH2A FEN1 CDK2 CHAF1A RRM1 MCM6 POLE up
fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='CANARY: G vs P')##
##
## |pathway | pval| padj| ES| NES| nMoreExtreme| size|leadingEdge |state |
## |:-------|----:|----:|--:|---:|------------:|----:|:-----------|:-----|
fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## -------------------------------- ---------- ---------- ----------- ---------- ------------- ----- --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------
## CYCLIN_D1_UP.V1_UP 0.0028653 0.0219870 -0.4137516 -2.018265 0 173 MASP1 TRPC3 SPOCK2 PTPN21 MUC5AC PDE1B SGCA EGR1 KLF4 THBD SLC19A1 SLC12A4 RRAS CA4 BMP1 RXRA CCL23 CEBPD GCHFR MSN SLN NEK3 APOA1 PKD1 FSHR TAGLN SCAP PLK3 DRD5 MSLN HK3 FAM189A2 TGFB1 CCIN CYP2A7 SMTN CD52 HTR6 STAT5A ZYX CXCR3 FOXO4 HSPG2 KCNAB2 ST3GAL4 SELPLG CHGA GLB1 ETS2 SHC3 ID1 RGR CTF1 COL4A2 RPS6KA1 KSR1 SYN1 ALDH3A2 CACNG1 PTMS CENPB DNASE2 PTS DMWD down
## SINGH_KRAS_DEPENDENCY_SIGNATURE 0.0018416 0.0219870 0.6639286 1.955218 0 19 C6orf141 TMEM45B LAD1 PRSS22 SEMA4B LAMC2 SDR16C5 AMPD3 MST1R DAPP1 up
## CSR_LATE_UP.V1_DN 0.0026596 0.0219870 -0.4063302 -1.920274 0 130 ACVRL1 GAS6 CLEC3B PLCD1 DENND2A MOB3C IRS2 APOL3 PAMR1 PDE5A VAMP5 GYPC HHEX C1orf115 LSS SFTPB MME ANKRD29 OLFML2A DAAM2 MRGPRF SGIP1 KIT ROBO3 TBC1D2B MVD MXD4 INSIG1 MAMDC2 ANGPTL2 CTSF KLHL29 BTG2 SUMF1 GAS1 DKK2 DRAM1 SC5D SVEP1 STARD4 TCEAL7 ABCA6 TMEM119 BACH1 NTN4 IDI1 ACKR4 TSC22D3 FADS1 EXOC6 COL8A2 LONRF1 ECH1 MSMO1 TNXB PGF FDFT1 GSN GFRA1 SOD2 GLT8D2 RASSF2 down
## PDGF_ERK_DN.V1_DN 0.0027624 0.0219870 -0.3983931 -1.907704 0 141 RTN2 TBX2 SMAD7 JUN EGR1 PER1 PNMT PNRC1 RHOB SULT1A1 DUSP1 THAP11 LTBP1 NFKBIA PHOX2B JUNB FRAT2 PDE4A HIC2 TMEM115 PDGFRA TGIF1 DUSP8 MAFF MBD3 SPRY2 MAP3K3 FZD2 CEBPB CDKN1B APC2 MGAT1 MON1B NCAPH2 EFNB2 DIP2A MAFG TRIB1 HAUS3 KLF10 C2CD2L TMEM11 ZNF324 PPP1R10 DNAJB1 CDK2AP2 BTG1 PISD TBKBP1 BRPF1 ANKRD40 PPP2R5B ANGEL1 MNT IRAK1BP1 ERF IL7R IDUA CIC USP33 SLC3A2 down
## CYCLIN_D1_KE_.V1_UP 0.0029155 0.0219870 -0.3557191 -1.740330 0 178 INPP5A MASP1 MUC5AC KLF4 THBD RRAS CA4 CCL23 CEBPD PPM1F GCHFR FGFR4 SLN NEK3 TGFBR2 PKD1 FSHR SCAP PLK3 DRD5 HK3 FAM189A2 PDE4C PKN1 LPIN2 GNAI2 SMTN CD52 HTR6 COX7A1 ZYX SNX17 HSPG2 APOA2 KLC1 KCNAB2 ST3GAL4 GLB1 NRG1 ETS2 ATXN1 PMPCA ARL3 ID1 KAT5 GLI1 ALDH3A2 BRF1 MAN2A2 CENPB PFKL DNASE2 PTS CELA2B DMWD CTBP1 MARK3 APOC1 TPTEP1 down
## MTOR_UP.V1_DN 0.0028653 0.0219870 -0.3439660 -1.675789 0 172 CSDC2 WFDC1 TSPAN4 SASH1 SCARA3 WIF1 SYN2 SLC12A4 TNNC2 AOC3 KCNC1 MYH11 KCNK3 FXYD1 KLF2 PPP1R14A IRS2 MYOC ADAMTS8 BACE1 DUSP1 PTGIS LIFR CRY2 PTGER4 LTBP1 C1QTNF4 PPP1R3C PALD1 CIRBP ITIH5 SULT2B1 PTPRS EFEMP2 ID2 PHC1 TNIP2 KAT6B RNF41 PI16 THBS3 KCNQ1 UBR3 DNASE2 CHST12 ABCA1 RFTN2 CSGALNACT2 down
## TGFB_UP.V1_UP 0.0028653 0.0219870 -0.3413239 -1.673709 0 176 SMAD6 TBX3 DLC1 JUN WNT11 LTBP2 WNT4 NDST1 KLF4 LMCD1 FLT4 RGCC RHOB SLCO2A1 TAGLN ABCG1 UBL3 ID3 JMJD6 HLX ATF3 CYP26B1 RCOR1 JUNB BMPR2 ZCCHC14 RGS11 SMTN NTF3 PLEKHA1 FOXF2 IL1RL1 TBC1D2B MAP3K4 ITGA5 RUSC2 JAM2 KANK1 PDGFB PXDC1 PHLDB1 ETS2 KDM6B SNAI1 NCOR2 MISP IL11 DACT1 CASP5 FERMT2 TFEB TRIB1 FAT4 PMP22 KLF10 PDGFA RGS12 RAPGEF2 PKIA PIK3CD LARP6 ANKLE2 down
## NOTCH_DN.V1_DN 0.0028653 0.0219870 -0.3438089 -1.663879 0 164 SLPI TBX3 PTCRA MAGEC3 MYO7B TRPC3 WIF1 ID4 INSM1 CA4 PSPN LRP4 KCNA5 RAMP2 KLF2 CPNE6 SLN FSTL3 CRH UTF1 CRMP1 SNED1 ITGA9 ADTRP ARHGAP6 TNFRSF8 FAT2 BAIAP2 HS1BP3 KLF15 TM4SF20 PBOV1 ATP8B3 SEMG2 CXCR3 GUCA2A ACADL PKD2L1 IFI30 FCGRT DCLK2 TMPRSS6 KCNE1 ID1 CHST1 LHX6 DRAM1 IL11 CD82 AMOTL2 ZBTB16 down
## PRC2_SUZ12_UP.V1_UP 0.0028986 0.0219870 -0.3429991 -1.657276 0 166 SLPI ACE PRKG2 KRT81 PTGIR AOC4P FOLR3 HBEGF TOM1L2 CBX7 MYL3 AATK DOK2 OTUB2 HIGD1B OR7E47P PDE6A AGO4 CDADC1 SLC15A3 ELANE C1orf21 FAT2 ZNF471 DACH1 STAT5A SST SMPD2 CXCR3 PKD2L1 OSTM1 SETBP1 PRKY LCAT ATXN1 GIMAP4 COL13A1 GAB2 FCN2 CAB39L MTMR10 FMNL1 PSMB8 CBL OPA3 TRIM58 down
## AKT_UP.V1_DN 0.0028653 0.0219870 -0.3397065 -1.657076 0 173 CSDC2 CDH16 TSPAN4 LIMD1 SASH1 SCARA3 WIF1 TNNC2 FMO2 HIC1 KCNK3 FXYD1 KLF2 IRS2 DPT MYOC RECK KCTD12 ID3 IFFO1 PTGIS GNMT TIMP3 ZEB1 PPP1R3C CAV2 ITIH5 PDGFRA STAT5A AXIN2 LPL GHR PDZRN3 EFEMP2 LTC4S CNN2 ZFYVE21 ITGBL1 CDPF1 SYPL2 TCF21 GAS1 DRAM1 ITPKB PI16 HEBP1 IL17RC CBS CHST12 down
## KRAS.BREAST_UP.V1_DN 0.0027027 0.0219870 -0.3506329 -1.626684 0 119 RAMP3 EGFL7 ALOX12B PDE6B MTHFR C22orf31 DPT DPEP2 APOL3 NOS1 SERPING1 CRH NAALADL1 ART1 MYL9 EPHX2 TSHB NTF3 ELMO1 TSPAN12 SELENBP1 SLC8A1 KRT38 MAST3 IL18R1 EDIL3 SCN7A TEX15 GJA4 RUNDC3B FGR NPR1 down
## PRC2_EED_UP.V1_DN 0.0028571 0.0219870 -0.3310876 -1.624062 0 179 CSDC2 WFDC1 KCNA4 PCDH12 TMEM59L TCAP NDRG4 SEMA3B SLC12A4 MCOLN1 CASKIN2 FASN HIC1 ARHGEF17 LIN7A HMOX1 PNPLA3 LMOD1 PEAK1 RAD54L2 MICAL1 LSS GNAI2 UTRN AFF3 FBXO17 ARRB2 CSPG4 RAPGEF1 MVD INSIG1 GSDMD MAPK7 XRCC3 RASSF1 SLC9A3R2 PDCD1LG2 GLI1 ITPKB MISP SYN1 MFHAS1 TRIM46 PACSIN3 PWP2 MAP3K6 SV2A ALG12 VAV2 TAF1C GPR176 DUSP7 ARHGAP19 TUBGCP2 PCDHGC3 SIPA1 DCSTAMP TCIRG1 ZNF446 PDE4D USP20 MRAS down
## LEF1_UP.V1_UP 0.0028571 0.0219870 -0.3288203 -1.612940 0 179 TULP2 ARC EGR2 WWC2 KRT81 NR3C1 WASF3 NES LTBP2 SCN5A CHGB TRPV2 C14orf132 RGCC RAI2 RAMP2 CCND2 FHL1 MSN FLNC AXL ADAMTS8 LMO2 KCTD12 TMEM47 MYL9 PARVB PDZD2 CYBRD1 FBXO17 FOXF2 S100A4 LPL TMOD1 GATA3 PLEKHF1 VIM ARID3B IL11 WNT5A TM4SF5 CBS PRF1 CST7 SYNE3 RRAGD PDGFA DLL3 GNG11 OBSL1 EMP3 FADS1 CD302 CEACAM21 CARD9 LOXL1 TGM2 PTGDS FN1 ADAM19 TMEM158 TNFRSF1B ZFPM2 COL6A1 CHST11 down
## RELA_DN.V1_UP 0.0026882 0.0219870 -0.3355831 -1.588031 0 131 SIRPB1 PPP1R15A JUN EGR1 FOSB THBD CST5 KLF6 ZFP36 PRDM11 PDE5A PRKG1 AGPAT4 FOS ATF3 KMO CYP26B1 JUNB TREX1 LHCGR FXYD7 DUSP8 USP9Y GPR85 VEGFB FGF2 FHL5 SNAI1 CTF1 CHST1 SLC27A6 CDHR5 CRB1 GNRH1 FGF17 KLF10 VDR NFIC KMT2D TRIM38 ZFP37 CLK1 LMO7 ZNF324 P2RY11 down
## RPS14_DN.V1_DN 0.0015314 0.0219870 0.3430808 1.582440 0 172 TUBB2B PCK1 SRD5A3 MCM10 LGR4 KIF20A NUP155 EXO1 TRIP13 PBK E2F8 TUBB2A EPCAM DEPDC1 TBRG4 CCNB2 CDC6 APOBEC3A NDC1 MKI67 TWISTNB PRC1 SLC29A2 ECT2 LLPH MSH2 SPTB ORC1 PSAT1 FBXO5 SH3TC2 ESPL1 KIF23 SLC25A21 PLK1 MCM5 TSPO2 SUV39H2 MYBL2 KIF15 NOC3L CRISP2 LRRC20 AGFG2 IL7 TLX2 STEAP3 EYA3 CDR2 EPB41 DDN KIF2C NLE1 CHAC1 DGCR11 GTF2H4 ZWILCH DNAJA4 ZNF74 PC APOOL GPATCH4 MANEA NMU ATAD2 MYO19 ERCC6L CAD RRS1 TUBG1 REPS2 CDC20 TRIM29 DLGAP5 RGS5 GATC RPUSD2 KLHL7 CA3 up
## RAPA_EARLY_UP.V1_DN 0.0028818 0.0219870 -0.3251195 -1.574973 0 167 PCSK2 TSPAN4 PRELP ENG SOX10 AOC3 PHYHIP FXYD1 PINK1 LMNA WFS1 AXL CRMP1 MINK1 CRY2 SYNGR4 GRN F10 PTCH1 CYP2A7 KRT4 ALDH1B1 CIT CCDC85B FAM49A PCBP4 IL11RA HAAO SMAD9 PSD SELPLG PRKCE LGALS3BP NR2F1 ACTR1B DPH1 KCNQ1 FAM168A FLT3LG PLEKHO2 ZNF175 IFI27 MAP1A HLA-E PTGS1 KRT17 PISD ATG2A TNN CACNB4 MTMR2 NAGPA GFRA2 GNAT1 MSMO1 down
## PIGF_UP.V1_DN 0.0028169 0.0219870 -0.3194307 -1.557284 0 169 ARC GPR17 NPAS3 PDE1B SPN AOC4P SLC14A2 TNFSF12 GPR37L1 BMP2 CCL16 PKD1 GYPC UTF1 OBSCN PDE6A MYL9 SMG6 GRIA1 BCAM DAAM2 CTSW S100A4 USP9Y NUCB1 ATP2B2 CEBPA MYO1F PDPN KCNAB2 CACNA1H CBFA2T3 FZD7 AURKC ADH1B IGFBP2 CTF1 SNX29 DHCR24 SVEP1 FCN2 CACNA1C VGF IRF2BP1 PXN APOC1 ACAT2 TPTEP1 KMT2D ALOX5AP PIK3R2 CD5 CCDC9 MCF2L NFKB2 MAP1A RPS4Y1 LOXL1 DPF1 PTGFR GRAP2 NOS2 C9 TMEM158 GFRA2 ANGEL1 AMELX down
## ESC_J1_UP_EARLY.V1_UP 0.0028571 0.0219870 -0.3183017 -1.531013 0 151 KANK3 FSCN3 DSCAM MAG C14orf132 IL36RN DBNDD2 PIK3R1 THRA ABCG1 ADCYAP1R1 DENND6A ADTRP TSHZ1 PTGER4 PHOX2B NAAA TPGS1 DLL1 PDK4 NAGLU BCL2L2 TLE6 FMNL3 CD33 RASL11B PDPN SOX15 CDKN1B DPP7 PHF21A DAB2 PRSS12 BNIPL HEY1 CD82 ZBTB16 AQP3 CRELD1 MPP2 down
## ESC_V6.5_UP_EARLY.V1_UP 0.0028902 0.0219870 -0.3186055 -1.527459 0 152 GPD1 CGNL1 SASH1 KLF13 SPOCK2 DLC1 OTUD7A ENG CA4 TTPA KCNC1 ARAP1 WNT3A VPS39 GRM8 ANKRD2 CYP27A1 ADAMTSL4 GPA33 SCAP TEX2 FGF5 FBP1 GPR153 DACH1 SMPD2 MAST3 NRL VEGFB RASAL2 ZNF865 PHF21A PRICKLE1 ARID3B ITIH3 TCEAL1 FBXW12 down
## STK33_UP 0.0032154 0.0219870 -0.2937783 -1.515673 0 263 EGR2 PPP1R15A CSRNP1 JUN EGR1 THBD OTUD1 HBEGF NLRC4 KLF6 ZFP36 RHOB OLR1 NKIRAS1 DUSP1 CD36 HMOX1 VSIG4 FOS FABP4 HECW2 KMO RTN1 ZEB2 MIR22HG CYBRD1 CD101 JUNB ZCCHC14 NCF2 PID1 TTLL7 MYOZ2 DAPK1 CPEB2 RIN2 PTPRO TGIF1 C20orf194 DUSP8 TNFSF15 C5AR1 CXCL3 MEIS3P1 DOCK4 GPRIN3 RNF149 HINT3 OSTM1 SETBP1 MAFF CFL2 CDKN1B BTG2 CREBRF ATXN1 RAB12 AKTIP WNT5A PPBP FAM20C WBP2 TFPI UNK CC2D1B ABCA1 CXCL2 TRIB1 AUH TYROBP NUAK1 SLC12A6 GNG11 FAM177A1 CDC37L1 ANXA1 down
## VEGF_A_UP.V1_DN 0.0030581 0.0219870 0.3240552 1.508384 1 184 DKK1 TSPAN8 ITGA2 ZNF117 NDC80 ATIC NUP155 DHFR EXO1 HMMR BUB1B TTK CRYZ CCNB1 LMNB1 STEAP1 CENPA BCL10 CCNB2 RRM2 MAPK6 MCM4 TWF1 UCHL3 UAP1 DHX29 DLEU1 NCOA3 BUB1 CDC45 SAT1 SLC4A7 KIF23 ASPH MBD4 MAD2L1 KIF11 RFC4 PSD3 XRCC4 RASA2 MAP1B DDX21 SERPINB2 KIF22 SPTLC2 EIF2S3 YES1 SPAG5 ITGB3 LRRC17 PRKACB SULT1B1 B4GALT5 ADAM9 ZC3H15 PRPF40A IL6 CDKN3 ATP13A3 LRP8 PLK4 MFAP3 BIRC5 RRS1 GPR37 SMC4 AMPH CKS2 CCNE1 DLGAP5 RGS5 HIRA CEBPZ RGS4 up
## STK33_NOMO_UP 0.0032573 0.0219870 -0.2911232 -1.506407 0 267 EPAS1 EGR2 PPP1R15A CSRNP1 JUN THBD OTUD1 KLF6 ZFP36 RHOB ULK2 OLR1 NKIRAS1 DUSP1 HMOX1 FOS ACP5 FABP4 HECW2 KMO KIFC3 ZEB2 MIR22HG JUNB ZCCHC14 PID1 MYOZ2 DAPK1 RIN2 MAP3K8 PTPRO TGIF1 C20orf194 TNFSF15 C5AR1 CXCL3 MEIS3P1 SLC24A3 DOCK4 GPRIN3 RNF149 HINT3 OSTM1 CD300C SETBP1 MAFF CLEC7A CFL2 FBXL13 BTG2 HSD11B1 CREBRF DAB2 C1QC RAB12 AKTIP WNT5A PPBP CADM1 CAB39L WBP2 DDIT4L UNK EFNB2 CC2D1B ABCA1 CXCL2 TBCEL GCNT2 TM6SF1 down
## ATM_DN.V1_DN 0.0027027 0.0219870 -0.3169688 -1.502503 0 132 ACVRL1 TCAP CLEC3B TEK HCRTR1 MAG PLCD1 ANGPT4 CRYBA1 GRM8 PRDM11 AZI2 CYP1A2 TAGLN CLCN4 F10 BMPR2 RDX LHCGR NEUROD1 RETN CXCL3 IL1RAPL1 HAAO PLA2G3 TXNRD2 CYBB KCNIP2 CES1P1 KCNE1 RAPGEF4 STX2 FCN2 NNAT WNT2 NLGN3 IFI27 TSPAN32 MS4A2 CSF2RB ADRB3 AGXT PPARGC1A MRAS TFEC SLC17A1 GDNF GRIN2D CHIA GMIP TEX14 RHAG RASSF9 XIAP down
## PRC2_EZH2_UP.V1_UP 0.0028653 0.0219870 -0.3053538 -1.497326 0 176 SLPI PRKG2 TMEM100 KLF13 RASL12 NES FOLR3 KLF4 HBEGF RGS16 AATK RGCC CDH13 PTPRB ART3 FXYD6 BMP2 OTUB2 PAMR1 KCTD12 CDADC1 NR4A2 FLVCR2 KCNA2 KLF11 TTLL7 GFPT2 GPM6B PAQR5 DUSP3 DUSP8 IL1RL1 SLC14A1 CORO2B OSTM1 SETBP1 ANGPTL2 COLEC10 FZD1 ATXN1 COL13A1 DKK2 down
## RAPA_EARLY_UP.V1_UP 0.0028571 0.0219870 -0.3042247 -1.458342 0 146 ARHGEF15 PDE1B PTGIR GREB1 TGM4 PRKCG PDE5A VSIG4 PLA2G5 BAP1 FRAT2 OLFML2A PDE4A TIMP2 LINC00563 ACOX3 HSPB6 SST USP9Y HERC3 CYP11B1 NUCB1 CEBPA NDST2 NRL CYP4A11 ITGA5 CTSF SCN2B CES1 SHC3 SLC25A42 FPGS AEBP1 CDON ATP2C2 P2RX7 CACNA1C VGF NCOA1 B3GNT6 TCTA SSH1 TRIM38 NKX2-8 ETV2 CCDC9 CLK1 PDE2A CTSD TNFAIP2 CDK10 down
## ESC_J1_UP_EARLY.V1_DN 0.0029070 0.0219870 -0.3010365 -1.442425 0 153 LIMS2 KLF13 EGR1 KLF4 CNN1 BMP1 EMP2 ZFP36 CEBPD TAGLN ID3 PTGIS CTRB1 MYL9 JUNB ANXA3 UBA7 TREX1 CIRBP ATP9B TLR9 UHRF1BP1L MAPK7 ZNF35 SOCS3 ID1 RRP8 MAPT MDN1 ARHGAP35 CENPB MVK TFEB DRD4 FGF17 FGF18 APOBR CCDC59 BRWD1 down
## WNT_UP.V1_DN 0.0028986 0.0219870 -0.2942710 -1.411420 0 155 RAMP3 KCNA4 ST6GALNAC6 TBXA2R THBD ADCY4 TRAPPC5 TGFBR3 RAI2 GPX3 GRM8 SYNGR4 TNFRSF8 F10 TSHB ADRB1 ST3GAL2 KCNA2 FOXN3 CDO1 SYT11 AARD MAPK7 FZD7 C16orf89 FBXO8 CD93 LGALS3BP TANC1 VIM HEY1 CASQ2 DPF3 ASH2L APC2 EFNB2 PLA2G1B ABCA1 GBP4 LHX1 HLA-A CD5 CYBA PLA2G10 CLN3 NMT2 NEO1 CD44 VEGFA CSF2RB down
## KRAS.600.LUNG.BREAST_UP.V1_DN 0.0031746 0.0219870 -0.2650662 -1.351851 0 244 PCSK2 RAMP3 CDH16 SCARF1 ALOX12B PDE6B MTHFR C22orf31 DPT APOL3 NOS1 SERPING1 CD36 NAALADL1 KCNMB1 ART1 FAM189A2 MYL9 CYP26B1 SH3GL3 RARRES2 EPHX2 TSHB GRIA1 OLFML2A KRT4 DAAM2 NTF3 EMID1 C5AR2 METTL7A ELMO1 NEUROD1 SELENBP1 CKM KRT38 MAST3 TYRP1 IL18R1 SCN7A TEX15 RUNDC3B PVALB LY6D KCNIP2 GAS1 KLK12 IGFBP2 CNTLN DGCR6L APC2 MXRA8 FGFR3 MRPL41 THBS3 down
## CSR_LATE_UP.V1_UP 0.0045662 0.0297591 0.3258526 1.484795 2 156 CXCL6 DCTPP1 YEATS4 FARSB TOMM34 CHEK2 TRIP13 FOXM1 PBK ANLN POLR3K CDCA8 ACTL6A CDK1 EEF1E1 NUF2 ILF2 GMNN ZWINT CDC6 RRM2 PAICS NDC1 NUDCD1 CLSPN CASP2 UMPS EZH2 CTPS1 TCF19 KRT18 NETO2 UHRF1 CCDC34 CMC2 EIF3B MCM3 MYBL2 RAD18 ITGA6 PRIM1 MTHFD1 AHSA1 CDC7 C19orf48 KIF22 RPF2 SMS DNAJB11 DCBLD1 ZNF367 YIPF3 POLE3 FEN1 ZWILCH up
## ESC_V6.5_UP_LATE.V1_UP 0.0056818 0.0355497 -0.2918800 -1.423661 1 170 SPOCK2 MYLIP RBP4 PTH1R CA4 FXYD2 TNNC1 MYL3 RAMP2 GPX3 BMP2 APOA1 SOX17 SOAT2 RECK SLC39A8 FGF5 ANKS1A LPIN2 FRAT2 PKDCC FOXA2 NAGLU SMPD2 UNC5B GATA6 PDZRN3 VEGFB PLAGL1 FZD2 RASAL2 CTDSPL GPC3 DCXR DAB2 PRSS12 BVES GAS1 PRICKLE1 PODXL ARID3B HEY1 COL4A2 STX2 GRIK5 down
fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## -------------------------------------------------------- ---------- --------- ----------- ---------- ------------- ----- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------
## GSE15750_DAY6_VS_DAY10_EFF_CD8_TCELL_UP 0.0014749 0.027915 0.5465044 2.496179 0 181 E2F7 SPAG1 CENPH HELLS MCM10 KNTC1 MUC20 NDC80 GINS1 KIF20A DHFR FIGNL1 STIL DNA2 HMMR PBK BUB1B CDCA8 TTK CDK1 NEK2 RBBP8 NUF2 RPA3 DEPDC1 PARPBP CENPM PMCH CENPA GMNN PSMG4 IQGAP3 CCNB2 RAD51AP1 CDC6 RRM2 FHL2 TIPIN PTPRK ASPM PSMD1 GTSE1 MELK C1orf112 RAD51B PRC1 LSM12 ASF1B NUSAP1 C12orf75 RACGAP1 STMN1 TPX2 KIF18B TCF19 BUB1 TOP2A CEP55 BRCA1 CDC25C UHRF1 FBXO5 ESPL1 PRDX4 MRPL9 CDC45 AURKB SPDL1 PASK KIF23 PLK1 MCM5 AURKA MAD2L1 MYBL2 CKAP2L KIF11 KNSTRN SKA3 PPIL1 POLQ MCM2 CENPW MCM7 ALDH7A1 KIF22 RAD54B CKS1B NCAPG CASP3 ESCO2 NEURL1B KIF2C TAX1BP3 SPAG5 up
## GSE21063_WT_VS_NFATC1_KO_8H_ANTI_IGM_STIM_BCELL_UP 0.0014641 0.027915 0.5387389 2.460484 0 178 ELOVL6 E2F7 KCNK5 LACTB2 YEATS4 MCM10 CDCA7 GPT2 NDC80 BDH1 DEPDC1B GMDS SLC27A2 INPP4B HJURP DHFR CHEK2 EXO1 TCEA1 BUB1B ANLN TTK UBE2T CDK1 SFXN1 E2F8 MNAT1 RBBP8 NUF2 CCNB1 PARPBP UCK2 CENPL MBOAT1 DTL TYMS TSPAN5 AP2B1 CDC6 TIPIN CDC25A ASPM MELK MKI67 CDCA2 PRC1 XPOT WDR12 ASF1B CCNE2 DLEU1 EZH2 ECT2 TPX2 KIF18B BUB1 TOP2A WDYHV1 PSAT1 TMEM106C FBXO5 VANGL1 AURKB MCM5 PIF1 AURKA ORC6 MAD2L1 SUV39H2 KIFC1 KIF11 RFC4 SRI IFI27L1 CHEK1 RHEBL1 KIF15 PRIM1 LRRC20 MTHFD1 PRPS2 ALG8 POLA2 up
## GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_UP 0.0014620 0.027915 0.5340132 2.459579 0 188 MND1 E2F7 KIF2A CENPH ITGA2 CENPK CCT2 MCM10 MUC20 KIF20A DHFR STIL DNA2 EXO1 FOXM1 HMMR PBK BUB1B ANLN TTK CENPF CDK1 E2F8 NEK2 NUF2 DEPDC1 PARPBP CENPM PMCH CENPA PCNA DTL CCNB2 RAD51AP1 FANCD2 CDC6 RRM2 GEN1 ASPM CDCA7L FAM221A RBMX CLSPN GTSE1 MELK MKI67 CDCA2 TICRR ECT2 RACGAP1 STMN1 TPX2 KIF18B TCF19 BUB1 ORC1 TOP2A CEP55 PSAT1 CDC25C UHRF1 CDC45 AURKB SPDL1 PASK KIF23 NUP205 PLK1 PIF1 AURKA CCAR1 MAD2L1 MCM3 MYBL2 CKAP2L KNSTRN CHEK1 SKA3 SYNRG EME1 PRIM1 CPOX CKAP5 KIF22 CDCA5 CKS1B NCAPG ESCO2 FAM114A1 CCNF SPAG5 SQLE NMRAL1 CENPI FEN1 PRSS16 ZWILCH KIF20B SPC24 CDKN3 SPC25 CCDC43 PRR11 BRIP1 AUNIP CENPP BIRC5 CTLA4 CKAP2 up
## GSE29614_CTRL_VS_DAY7_TIV_FLU_VACCINE_PBMC_DN 0.0014599 0.027915 0.5197396 2.369813 0 172 KLHL14 SEL1L3 GPT2 IGLV3-19 CLINT1 GINS1 DENND5B TNFRSF13B TRIP13 FOXM1 HMMR PBK BUB1B ARNTL2 TTK CENPF CDK1 E2F8 NUF2 PTTG1 SLC41A2 CCNB1 PARPBP KIF14 STT3A TPD52 CCDC113 DTL EAF2 CCNB2 TYMS ZWINT CDC6 RRM2 GEN1 CLPTM1L C11orf80 POU2AF1 MELK MKI67 SPATS2 SEC24A NUSAP1 UGT2B17 IGLL3P IGKV1D-13 TPX2 BUB1 CEP55 FBXO5 SUB1 SPCS1 SDHA PRDX4 GLDC AURKA SSR3 SDC1 KIF11 CHEK1 CD38 CBWD1 KIF15 MCM2 FKBP14 MTHFD1 FAM98A MRPL35 OSTC TNFRSF17 SLC2A5 MYO1D RASGRP3 BFSP2 SRPRB CREB3L2 NCAPG IGHM LMAN1 SLC30A5 DNAJB11 MCEE SPAG5 C11orf24 NT5DC2 CENPI CEP128 SRP54 RPN2 CDKN3 XBP1 MANEA EFHC1 VOPP1 UBE2J1 TUBG1 MZB1 CHAC2 CDC20 IGKV3-20 B4GALT3 DLGAP5 SLC44A1 up
## GSE36476_CTRL_VS_TSST_ACT_72H_MEMORY_CD4_TCELL_YOUNG_DN 0.0014620 0.027915 0.5127610 2.353305 0 183 ELOVL6 DCTPP1 MCM10 BDH1 NME1 IL1R2 KIF20A DHFR STIL FOXM1 HMMR PBK BUB1B MED14 CDCA8 ARNTL2 TTK RBBP8 APOLD1 PTTG1 LGMN CCNB1 RPA3 CENPM FANCI STT3A CENPA GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT CDC6 RRM2 PAICS CDC25A ASPM MKI67 NUSAP1 SRSF1 UMPS SFT2D2 AIMP2 STMN1 MYCBP CTPS1 BUB1 TOP2A CEP55 TMEM106C FBXO5 ESPL1 CISD1 TTF2 CDC45 MCM5 AURKA MIS18A GBAP1 KIFC1 KIF11 RFC4 FANCL CHEK1 BATF POLQ KIF15 MCM2 MYOF MRPL35 POLA2 MCM7 CKAP5 CKS1B NCAPG KIF2C TRAIP POLE2 SPAG5 NQO1 TPGS2 RPP40 PGAM1 PSMB2 FEN1 UBFD1 RAD54L CDKN3 C3orf14 POLR2H ZNF248 GPR19 ERCC6L DPP3 BIRC5 TUBG1 CDC20 CKS2 GCNT1 DLGAP5 FH up
## GSE29618_BCELL_VS_MONOCYTE_DAY7_FLU_VACCINE_DN 0.0031447 0.027915 -0.4661649 -2.341181 0 188 SIRPB1 SLC31A2 HBEGF ARRB1 AHNAK STX11 TNFSF12 RGCC RXRA CEBPD EIF4A1 ULK2 GAA LMNA SULT1A1 LIN7A PHACTR2 HMOX1 ARAP3 ALDH2 ATF3 TNFSF13 GRN RTN1 RCOR1 MIR22HG FLVCR2 TIMP2 PILRA PID1 DAPK1 ZYX SIRPA NACC2 SULT1A2 FBXL5 BST1 GNAQ C5AR1 EMILIN2 MCL1 ALDH3B1 CEBPA MYO1F ID2 GABARAPL1 FCGRT LRPAP1 HDAC4 FZD1 SORT1 CD4 VIM DOCK5 CST3 IL17RA TRIB1 PXN ST3GAL6 APOBR KLF10 TYROBP RRAGD KIAA0513 FTL CTSD ITM2B SIGLEC9 ERMAP HCAR3 PSTPIP1 CD302 SLCO3A1 CAMKK2 VEGFA PGD ARHGEF40 CD163 WDFY3 TNFRSF1B VPS37C ZNF467 GABARAP GNA15 NLRP3 IMPA2 TIAM1 SEMA4A down
## GSE22886_UNSTIM_VS_IL15_STIM_NKCELL_DN 0.0014641 0.027915 0.5100587 2.335610 0 182 ELOVL6 DCTPP1 GGCT CCT2 MCM10 BLM MRPS35 NME1 MAT2A MRPL15 XRCC5 TRIP13 CDK4 PBK POLR3K CCT5 SFXN1 EEF1E1 RBBP8 CCT6A POLD2 RPA3 VDAC1 CPD GMNN PCNA APOO DTL GLRX3 RAD51AP1 CDC6 PAICS MCM4 TIPIN ASCC3 PRC1 XPOT WDR12 GNL2 CTPS1 TOPBP1 ORC1 CDC45 HSPA14 ENO1 NUP205 MCM5 BCL2L1 DCLRE1A MAD2L1 SHMT2 SUV39H2 RFC4 UGDH CCT8 MCM2 MTCH2 MTHFD1 MRPL35 PGRMC1 MCM7 MRPS15 DNAJC9 CKS1B MSH6 PRDX3 HSPD1 CDT1 MRPL17 SQLE SNRPG SLC1A4 SLCO4A1 RANBP1 ZMPSTE24 FEN1 ARMC1 PSMC4 CDK2 EIF2S1 PAK1IP1 CCT7 POLR2H SNRPB DPP3 PSMB5 RAN TUBG1 SMC4 UBA2 PA2G4 CDC20 CKS2 LTA NIPA2 STIP1 MCM6 FH HAT1 HNRNPAB PPAT ENOPH1 EIF3J CSE1L MLEC UBE2S ALG5 up
## GSE36476_CTRL_VS_TSST_ACT_40H_MEMORY_CD4_TCELL_OLD_DN 0.0014684 0.027915 0.5032880 2.308447 0 186 DCTPP1 SRPK1 MCM10 BLM BDH1 NME1 IL1R2 KIF20A HJURP MRPL15 DHFR TRIP13 CDK4 HMMR BUB1B POLR3K TBC1D8 CENPF CCT3 CCNB1 RPA3 UCK2 CENPM FANCI CENPA DTL NIT2 CCNB2 TYMS RAD51AP1 PHLDA1 ZWINT CDC6 RRM2 PAICS MCM4 CDC25A ASPM MELK GAPDH HCP5 SFT2D2 AIMP2 RACGAP1 STMN1 CTPS1 TPX2 IRF4 NUDT1 TOP2A CEP55 IER3 TMEM106C ESPL1 AURKB SPDL1 PHB AURKA CSTF2 KIF11 RFC4 CHEK1 KIF15 MCM2 PRIM1 MTHFD1 MRPL35 LRRC42 MCM7 ZNF189 CKAP5 RMI1 RBX1 CKS1B NCAPG KIF2C TRAP1 POLE2 SPAG5 GOT2 SPRED2 UNG SLCO4A1 RANBP1 PGAM1 ME2 WDR76 RNASEH2A FEN1 SPATS2L POLR2H IDH1 DPP3 PSMB5 TUBG1 MRPL11 RAD51C CKS2 NCAPG2 DLGAP5 STIP1 FH ARFIP1 RAD51 BCL2L11 GART TP53BP1 TUBA1C ETNK1 up
## GSE29614_DAY3_VS_DAY7_TIV_FLU_VACCINE_PBMC_DN 0.0014599 0.027915 0.5046557 2.301799 0 173 TLR10 KLHL14 TEX9 KDELR2 SEL1L3 IGLV6-57 GPT2 PERP IGLV3-19 GINS1 DENND5B STIL TNFRSF13B TRIP13 HMMR PBK BUB1B CD180 SLC35F2 CDK1 E2F8 NUF2 PTTG1 CCNB1 FCRL5 CENPM UGT2B15 SLC16A14 TPD52 CCDC113 EAF2 TIGD6 CCNB2 CDC6 RRM2 GEN1 CLPTM1L C3orf52 C11orf80 FAIM POU2AF1 MKI67 SPATS2 SEC24A UGT2B17 IGLL3P IGKV1D-13 OSBPL10 BUB1 UQCRH SUB1 PRDX4 GLDC PHB SSR3 PNOC SDC1 DOCK3 CHEK1 CD38 CBWD1 NOC3L FKBP14 SP140 OSTC TNFRSF17 SLC2A5 RASGRP3 SLC35F5 SRPRB NCAPG IGHM LMAN1 HSPD1 DNAJB11 MCEE SPAG5 SNRPG NT5DC2 CENPI PHGDH CEP128 FKBP3 SRP54 RPN2 STK19 CDKN3 XBP1 EFHC1 VOPP1 ARL1 UBE2J1 MZB1 CHAC2 CDC20 IGKV3-20 CXXC5 B4GALT3 DLGAP5 SLC44A1 up
## GSE24634_TEFF_VS_TCONV_DAY7_IN_CULTURE_UP 0.0014493 0.027915 0.4973139 2.299825 0 192 STK39 MCCC2 HELLS FUT8 SRPK1 KNTC1 PMS2P5 BLM NDC80 SLC27A2 KIF20A HJURP P2RX5 STIL TRIP13 HMMR CDCA8 CENPF CD79B CDK1 RBBP8 STS PTTG1 CCNB1 CENPM FANCI PMCH OLA1 CENPA GMNN PCNA DTL CCNB2 RAD51AP1 TSPAN5 ZWINT RRM2 MCM4 SMC6 ASPM MELK GMPS PRC1 NUSAP1 RACGAP1 STMN1 CTPS1 TPX2 STAU2 TDP1 GOLGB1 NUDT1 CEP55 CDC25C ESPL1 CDC45 PLK1 AURKA DCLRE1A MAD2L1 KIF11 RFC4 CCR8 CD38 POLQ KIF15 MCM2 RBMX2 SP140 PRIM1 SIRPG RAB27A FGFR1OP CD96 POLA2 TIMELESS MCM7 CKAP5 KIF22 CDR2 CREB3L2 FASTKD3 NCAPG SNRPD1 CLEC2D KIF2C CDT1 CBLB IFT52 VIPAS39 TPGS2 PHGDH FEN1 MPHOSPH9 RAD54L CSF2 MANEA CCR4 PLK4 CTLA4 MRPL11 CDC20 CKS2 IDH2 CCNE1 SYNGR3 DLGAP5 MCM6 CAPN2 RAD51 FAF1 SLC9A3R1 up
## GSE14415_TCONV_VS_FOXP3_KO_INDUCED_TREG_DN 0.0014409 0.027915 0.5059391 2.295114 0 160 DCTPP1 CENPH KNTC1 MPP6 GINS1 FIGNL1 TCERG1 TRIP13 PBK BUB1B CDCA8 CDK1 E2F8 WDHD1 NUF2 THYN1 KIF14 CENPA DTL CCNB2 RRM2 GATM TIPIN GEN1 LRRC59 PPP1R8 CLSPN PRC1 ECE1 COX7A2 RACGAP1 IGF2BP3 STMN1 TPX2 NUDT1 BUB1 PSPH NOP2 CEP55 ERH BRCA1 CDC25C UHRF1 CDC45 KIF23 PLK1 AARSD1 MAD2L1 MCM3 KIF11 CHEK1 FAM49B AP1S1 MTHFD2 KIF15 MCM2 RAB27A PPA1 CDC7 DDX21 UBR7 ZMAT2 SNRPA NCAPG LMAN1 PRDX3 NCAPD2 ALDOA WDR76 SAE1 CDK2 SPC24 ATAD2 SNRPB PLK4 RBM8A SYNGR2 ANAPC5 AHCY BRIP1 SLC35A5 CENPP BIRC5 DSCC1 PLAC8 TAF1D PA2G4 NCAPG2 PMF1 DLGAP5 RRM1 MCM6 LANCL2 SMAP2 IRAK3 ATAD5 PDIA3 PSMD8 KLHDC10 PIGT ANP32E SMC2 CCNA2 NAA50 CBX5 PPP4C AK2 FPR1 SNX5 API5 up
## GSE36476_CTRL_VS_TSST_ACT_72H_MEMORY_CD4_TCELL_OLD_DN 0.0014749 0.027915 0.5010202 2.288428 0 181 TUBB2B MCM10 BLM BDH1 NME1 KIF20A HJURP MRPL15 TRIP13 CDK4 FOXM1 HMMR BUB1B CENPF RBBP8 CCT3 CCNB1 UCK2 CENPM FANCI CENPA DTL NIT2 CCNB2 TYMS ZWINT CDC6 RRM2 PAICS MCM4 ASPM MELK MKI67 NUSAP1 SRSF1 RACGAP1 STMN1 CTPS1 TPX2 CCT4 IRF4 NUDT1 SNRNP25 TOP2A CEP55 TMEM106C SMARCAL1 ESPL1 AURKB KIF23 MCM5 AURKA MIS18A CSTF2 KIF11 RFC4 MCM2 METTL5 MYOF MTCH2 MTHFD1 TIMELESS MCM7 NDUFS2 ZNF189 POLD3 CKAP5 CKS1B NAP1L4 HAUS4 NCAPG POLE2 SPAG5 GOT2 CLTC RAB33A UNG SLCO4A1 GTF2H4 PGAM1 PSMB2 RNASEH2A FEN1 ZWILCH ICMT TRIM32 LIMA1 GNPDA1 PLK4 PCCB DPP3 PSMB5 TUBG1 FOCAD MRPL11 CDC20 RAD51C NCAPG2 CCNE1 DLGAP5 FH HNRNPAB RAD51 GART TP53BP1 up
## GSE24634_TREG_VS_TCONV_POST_DAY5_IL4_CONVERSION_UP 0.0014620 0.027915 0.4931173 2.263151 0 183 CEACAM1 ELOVL6 OSBPL3 KNTC1 BDH1 HJURP BRIX1 TCERG1 EXO1 TRIP13 POLR3K TTK HEATR1 SLC35F2 NEK2 CCT6A UCK2 ILF2 TPD52 MAGOHB PUS7 AP2B1 PAICS TIPIN UCHL3 PON2 MKI67 GEMIN6 GMPS RBBP4 GTPBP4 EZH2 RAD50 TDP1 PRPS1 ERH BRCA1 HSPA14 SNRNP40 PHB PLK1 CSTF2 SUV39H2 MYBL2 RFC4 CENPQ POLQ RAD1 DUS4L SP140 PRIM1 PSMB4 LRRC42 INPP1 POLR2D CCDC88C FAHD2A TMEM258 DNAJC9 HCCS UBR7 SMS NCAPD2 DGUOK TRAIP CDT1 PSME3 ABCE1 PTBP3 EIF5B SLCO4A1 RWDD2B POLE3 SNRPC RNASEH2A SUPT16H ICMT TFB2M RRP15 CCT7 C19orf53 SEPHS1 ERCC6L CAD NFATC2IP KDM1A MRPL11 NCAPD3 PPID LANCL2 SLC25A32 ZW10 RAD51 PPAT TIMM10 GART PSMA3 up
## GSE18893_TCONV_VS_TREG_24H_TNF_STIM_UP 0.0014599 0.027915 0.4953586 2.259394 0 173 E2F7 HELLS KNTC1 CDCA7 PRIM2 DEPDC1B SLC27A2 GINS1 NUP155 FIGNL1 TROAP C1orf131 ACTL6A PTTG1 ILF2 GMNN PCNA APOO CDC23 NIT2 RAD51AP1 CDC6 MCM4 CDC25A CMTM1 SFXN4 ETFA PRKDC PKP4 CCNE2 BTF3 TICRR RACGAP1 PDZD11 MRPS18A TCF19 NUDT1 MSH2 CLIC1 BRCA1 UHRF1 FBXO5 SPCS1 BOLA3 CCDC34 HSPA14 COQ3 MYBL2 RFC4 KIF15 MCM2 ERI2 TTLL12 MRPL35 POLA2 TPRKB MCM7 CABLES2 FAHD2A TMEM258 C19orf48 CDCA5 NDUFB3 CKS1B NDUFA2 MSH6 RTCB ESCO2 MRPS21 TRAP1 CCNF CDT1 SLC37A4 GOT2 VPS25 NMRAL1 TPGS2 RANBP1 BUB3 RNASEH2A CHCHD2 ZWILCH TRIM59 CDK2 SPC24 NDUFA8 ERCC6L CAD BRIP1 COX6C SDHB CKS2 COQ9 RRM1 NUP35 up
## GSE24634_TREG_VS_TCONV_POST_DAY7_IL4_CONVERSION_UP 0.0014620 0.027915 0.4902277 2.249889 0 183 ELOVL6 FUT8 KNTC1 SPRR3 BLM GINS1 HJURP DHFR P2RX5 EXO1 TRIP13 CDCA8 CENPF CD79B SLC35F2 WDHD1 RBBP8 PTTG1 CCNB1 RPA3 CENPM FANCI LMNB1 CENPA GMNN UQCRQ DTL CCNB2 TYMS ZWINT RRM2 MCM4 MELK C1orf112 PRC1 PKP4 NUSAP1 AGK DLEU1 EZH2 TPX2 IRF4 BUB1 SNF8 CEP55 TMEM106C COX10 GGCX CDC45 AURKB AURKA DCLRE1A SHMT2 CSTF2 MYBL2 KIF11 RFC4 DPEP1 CCR8 CD38 KIF15 RAD1 MCM2 RALGPS1 SP140 MCM7 CDC7 KIF22 CKS1B IGHM PTGDR2 KIF2C CDT1 SPAG5 RPL39L RCC1 TPGS2 SLCO4A1 KLHL25 WDR76 RNASEH2A FEN1 SEC61A2 ZWILCH UBFD1 CDKN3 ATAD2 PLK4 GPR19 DPP3 BIRC5 MRPL11 CDC20 CKS2 NCAPG2 PTPRN2 IDH2 DLGAP5 PDZK1IP1 LANCL2 MRPS12 HNRNPAB RAD51 up
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_DN 0.0031546 0.027915 -0.4450512 -2.243844 0 191 TBC1D2 ABHD5 SLC31A2 RXRA CEBPD ZMIZ1 ARAP1 CD36 KCTD12 MANBA KCNMB1 HK3 ATG7 TNFSF13 FBP1 GRN FKBP15 RTN1 SLC11A1 SH2B3 SLC15A3 HS1BP3 CORO1C FLVCR2 NCF2 TIMP2 MTMR14 PILRA FAM49A ZFAND5 DAPK1 RIN2 SIRPA DUSP3 BCL2L2 CD33 DIAPH2 IFI30 CLEC7A PLAGL1 PTAFR COQ2 SLC7A7 SNX10 CEBPB GLB1 CYBB FGR CD93 GAB2 TBC1D12 GCA MNDA PTPRE ASAH1 MGAT1 STX7 SCPEP1 CCDC88A DEF8 ATP6V1B2 APOBR PTTG1IP BACH1 CASP1 OAZ1 FTL TNFAIP2 SIGLEC9 PTGS1 EXOC1 SH3TC1 PISD CAPG PGD CSF2RB ARHGEF40 TNS3 down
## GSE37605_FOXP3_FUSION_GFP_VS_IRES_GFP_TREG_C57BL6_UP 0.0031348 0.027915 -0.4497268 -2.232004 0 179 ACO2 SIK1 EGR2 WWC2 PPP1R15A CSRNP1 NR4A1 JUN EGR1 PER1 FOSB LATS2 HBEGF TNS1 GEM ARL4D VSTM4 ZFP36 CEBPD PTPRM HOXA5 JDP2 ESAM DUSP1 ID3 PLK3 FOS ATF3 JUNB NR4A2 DLL1 FLVCR2 TGFB1I1 CYYR1 SLCO2B1 NTF3 ZFYVE9 FOXN3 DAPK1 SLC25A25 TSPAN12 RCAN1 SLC24A3 RASL11B CMKLR1 MAFF SPRY2 CD151 FZD7 CEBPB CNTFR BTG2 NBL1 CD93 ETS2 KDM6B ID1 OSTF1 CCRL2 RASGEF1B SVEP1 MFHAS1 NR4A3 NDRG2 H6PD CXCL2 down
## GSE14415_INDUCED_VS_NATURAL_TREG_DN 0.0014493 0.027915 0.4884327 2.224184 0 166 GDA DCTPP1 CENPH TEX9 CDCA7 MPP6 DEPDC1B NME1 GINS1 EXO1 TRIP13 HMMR PBK BUB1B CDCA8 TTK CENPF CDK1 E2F8 WDHD1 NUF2 KIF14 LMNB1 CENPA CCNB2 TIPIN GEN1 TTC9C NUDCD1 ASPM CLSPN MELK MKI67 ASF1B IL1RL2 EZH2 ECT2 IGF2BP3 STMN1 TPX2 NUDT1 BUB1 TOP2A CEP55 BRCA1 CDC25C ADAP1 CDC45 KIF23 PLK1 MCM5 AARSD1 MCM3 CKAP2L KIF11 KIF15 MCM2 ALG8 UBR7 CKAP5 KIF22 MPO CKS1B NCAPG LMAN1 LGALS3 PRDX3 HSPD1 KIF2C ALDOA ITGB3 SAE1 CANX RAD54L SPC24 NOL12 PLK4 ANAPC5 NR1I3 ISOC1 BIRC5 PLAC8 TAF1D NCAPG2 PMF1 DLGAP5 RRM1 LANCL2 ERAP1 RAD51 HDAC3 GPR55 ATAD5 SEH1L PDIA3 PSMD8 POLA1 PIGT SMC2 CCNA2 up
## GSE36476_CTRL_VS_TSST_ACT_40H_MEMORY_CD4_TCELL_YOUNG_DN 0.0014684 0.027915 0.4813591 2.209824 0 187 KCNK5 DCTPP1 SRPK1 MCM10 PALB2 BLM NME1 SORD IL1R2 KIF20A HJURP DHFR AIM2 TRIP13 HMMR CDCA8 RBBP8 LGMN CCNB1 RPA3 UCK2 CENPM STT3A CENPA PCNA DTL PUS7 CCNB2 TYMS RRM2 PAICS MCM4 ASPM UQCC1 MKI67 NUSAP1 CCNE2 SRSF1 UMPS AIMP2 RACGAP1 LIG3 STMN1 CTPS1 TPX2 KIF18B IRF4 TOP2A CEP55 BRCA1 CDC25C TMEM106C IL12RB2 CCL22 ESPL1 GALE CISD1 PRDX4 CDC45 VANGL1 AURKB KIF23 MCM5 GBAP1 KIF11 RFC4 BATF MCM2 MYOF MRPL35 POLA2 MCM7 CKAP5 CKS1B NCAPG KIF2C POLE2 SPAG5 NQO1 SPRED2 ACY1 SLCO4A1 PGAM1 FEN1 ZWILCH RAB38 RAD54L CDKN3 C3orf14 CHAF1A BIRC5 CTLA4 TUBG1 CDC20 CKS2 NCAPG2 CCNE1 GCNT1 STIP1 FH up
## GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN 0.0031746 0.027915 -0.4332957 -2.182068 0 190 SH2D3C GIMAP8 KLF13 LTBP2 FRAT1 NDST1 ARRB1 ENG PPM1F GIMAP1 PECAM1 PINK1 SGK3 NCKAP5L CXCL16 APOL3 TGFBR2 IFFO1 ACP5 GRN DSTYK SUN2 ELMSAN1 MYD88 NISCH MAST3 HECA MYO1F GRB2 PTAFR HCK MAP3K3 NFAM1 ARRDC2 CYBB CFP GLTP ARL3 NLRP12 WBP1L C1orf162 TACC1 ZNF710 SEC14L1 MGAT4A RPS6KA1 TNFAIP8L2 ARHGAP30 CRTC3 BRD3 PIK3R5 CALHM2 PPP1R9B FAM78A USP19 SETD1B IL27RA TFEB ZNF740 TTC7A SYNE3 PTTG1IP down
## GSE13547_2H_VS_12_H_ANTI_IGM_STIM_BCELL_DN 0.0014577 0.027915 0.4785813 2.180332 0 169 MRPL46 MCM10 PRIM2 NME1 GINS1 ANXA2 FIGNL1 TROAP TRIP13 CDK4 HMMR PBK POLR3K ACP1 CDCA8 CDK1 SFXN1 FAM136A COPS5 NUF2 DEPDC1 UCK2 NME7 GMNN CCNB2 RAD51AP1 RRM2 NDC1 GEN1 MKI67 LSM12 SLC25A13 ASF1B RBBP7 CDC123 STMN1 MRPS18A IRF4 BUB1 TIMM17A SNF8 ERH PSAT1 FBXO5 ADAP1 CCDC34 CDC45 AURKB AGPAT5 SPDL1 PLK1 AURKA ORC6 MAD2L1 SHMT2 CSTF2 CKAP2L KIF15 EME1 NHP2 PRIM1 PSMA5 MCM7 PPA1 PRKAG1 KIF22 CKS1B DPAGT1 POLE2 SPAG5 BCKDK RCC1 RANBP1 BUB3 PSMB2 EIF2S2 SPC24 CDKN3 SPC25 GZMK CENPP ISOC1 RAN BIRC5 SDHB DSCC1 TUBG1 PLAC8 PMPCB up
## GSE24574_BCL6_LOW_TFH_VS_TCONV_CD4_TCELL_DN 0.0014620 0.027915 0.4748958 2.179524 0 183 GGCT BLM BDH1 SLC27A2 GINS1 SORD MAT2A DHFR CDK4 HMMR BUB1B TTK CENPF CRYZ EEF1E1 CCT6A RPA3 FANCI NIPSNAP1 TYMS RAD51AP1 ZWINT MCM4 S100A11 MELK XPOT PARP1 GAPDH UMPS EZH2 CLIC1 ORC1 NDUFB8 TOP2A XCL2 ESPL1 GALE PKM TTF2 AURKB TBCE ENO1 PLK1 AURKA SHMT2 MCM3 MYBL2 KIFC1 PITPNB RFC4 FANCL MTHFD2 TP53 MCM2 PRIM1 MTHFD1 PSMA5 FAM98A PRPS2 FAM161A POLD3 CDC7 CPOX ST14 CKS1B COX6A1 SNRPA SMS AHCYL1 NCAPD2 PNP TRAIP UNG PHGDH SNRPC SEC23IP RAD54L CDK2 EIF2S1 AIFM1 GSTP1 HAX1 PLK4 CHAF1A TUBG1 LDHA PPID IDH2 GOSR2 up
## GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_DN 0.0032051 0.027915 -0.4317468 -2.178463 0 192 TBC1D2 ZCCHC24 ASGR1 SLC31A2 KLF4 CFD BEST1 MCOLN1 RXRA ZMIZ1 DOK2 GAA PECAM1 MARCO CD36 KCTD12 HMOX1 KCNMB1 HK3 ALDH2 ATG7 FBP1 LAMP1 SLC11A1 FLVCR2 NCF2 PILRA DAPK1 LRP1 EPB41L3 RIN2 SIRPA NACC2 ARRB2 S100A4 GNAQ C5AR1 ALDH3B1 CEBPA MYO1F ITGA5 CLEC7A FCGRT SLC7A7 CEBPB CFP CD93 ETS2 FHOD1 SPG21 PTPRE CST3 HEBP1 ATP6V1B2 ST3GAL6 APOBR TYROBP FCGR1B RRAGD PTTG1IP TSPO KIAA0513 FTL P2RY2 CTSD TNFAIP2 SLCO3A1 CARD9 RHOG TMEM164 ARHGEF40 CD163 WDFY3 ASB13 TNFRSF1B VPS37C CAMK1 GNA15 NLRP3 BLVRB RTN4 ITGAM SLC16A5 TCF7L2 FCER1G MAFB OAZ2 CSF3R RAB31 down
## GSE42088_2H_VS_24H_LEISHMANIA_INF_DC_UP 0.0030769 0.027915 -0.4366838 -2.175880 0 180 INPP5K JUND ZCCHC24 NR4A1 KLF4 CARS2 RPS9 RAB11FIP1 ZFP36 PPM1F PECAM1 KLF2 DPEP2 NLRP1 HMOX1 MINK1 FOS YPEL5 ALDH2 MPPE1 FBP1 NR4A2 ALOX5 CRTAP CD52 TIMP2 MYD88 LTA4H LRRFIP1 ARRB2 BST1 S100A4 C5AR1 MKNK2 KCNAB2 MPC1 FCGRT CNN2 VPS51 SELPLG CD4 TACC1 THEMIS2 MNDA ASAH1 KCNQ1 MAN2A2 CST3 SCPEP1 PXN CCDC69 MXI1 HSD17B11 CELF2 TSPO RPL21 ITGB2 PLP2 KIAA0513 CTSD ITM2B TSC22D3 CRBN PYCARD CD302 EIF3F PLD3 SH3TC1 down
## GSE39556_CD8A_DC_VS_NK_CELL_MOUSE_3H_POST_POLYIC_INJ_UP 0.0014556 0.027915 0.4708282 2.162600 0 185 LINC00342 LAGE3 CLGN COCH KNTC1 PRIM2 BLM NDC80 SLC27A2 GINS1 APOBEC3B NUP155 DHFR CHEK2 TROAP STIL DNA2 NET1 EXO1 TRIP13 FOXM1 HMMR BUB1B TTK CDK1 NEK2 RBBP8 CCNB1 KIF14 FAM153B FANCI CENPA CCNB2 RAD51AP1 ZWINT CDC6 RRM2 PAICS HLTF GTSE1 MELK GMPS GPSM2 CCNE2 UMPS DLG3 TPX2 STAU2 NUDT1 BUB1 TOP2A BRCA1 CDC25C TMEM106C SKP2 ESPL1 GALE CDC45 KIF23 NUP205 AURKA KIF11 RFC4 FANCL CHEK1 MTHFD2 ERI2 PRIM1 MTHFD1 GBA FGFR1OP PRPS2 TIMELESS ALDH7A1 CDC7 KIF22 CKS1B XRCC2 KIF2C CCNF POLE2 SLC37A4 SPAG5 RPL39L BARD1 STK3 PHGDH RNASEH2A KIF20B AP3B1 ICMT CDK2 CDKN3 PLK4 CHAF1A PKMYT1 TUBG1 SMC4 CDC20 PIK3R3 CKS2 NCAPD3 CCNE1 DLGAP5 RRM1 POLE KIAA0586 up
## GSE29618_MONOCYTE_VS_PDC_DAY7_FLU_VACCINE_UP 0.0032051 0.027915 -0.4283966 -2.161559 0 192 EGR1 SLC31A2 HBEGF ARRB1 BEST1 RXRA CEBPD PPM1F MSN DPEP2 APOL3 LIN7A DENND3 SERPINB6 HMOX1 ARAP3 TNFSF13 RTN1 ALOX5 FLVCR2 YBX3 NCF2 LTA4H PILRA KLF11 PID1 EPB41L3 RIN2 SIRPA NACC2 TGIF1 FBXL5 C5AR1 CD33 ALDH3B1 CEBPA MYO1F IFI30 CLEC7A HCK SLC7A7 CEBPB FGR CD93 GMFG SPG21 DOCK5 ALDH3A2 ASAH1 SCPEP1 TRIB1 PXN DOK1 HSD17B11 CASP1 ITGB2 KIAA0513 FTL TNFAIP2 ITM2B HCAR3 PSTPIP1 MEGF9 CD44 SLCO3A1 SNX2 TMEM164 VEGFA ARHGEF40 CD163 WDFY3 SH3BP2 PLBD1 TNFRSF1B VPS37C TMBIM1 NLRP3 BLVRB ITGAM EIF4EBP2 SOD2 TCF7L2 SGK1 MAFB PYGL FCN1 CSF3R TREM1 ALDH1A1 RALB CD244 CD14 NPL ACSL1 down
## GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH1_DN 0.0014451 0.027915 0.4650507 2.146887 0 189 KCNN4 ELOVL6 CCT2 GNG4 MRPL15 SNRPE BET1 DNA2 PDCD6 MRPL33 POLR3K ACTL6A CSTF1 SFXN1 GTF2A2 EEF1E1 CCT6A CCNB1 DHDDS GMNN PCNA ST8SIA4 TBRG4 SLC25A44 TYMS UCHL3 PPP1R8 PSMD1 UCHL1 PRC1 XPOT UMPS RAD50 RACGAP1 MYCBP IRF4 IER3 TMCO1 SNRNP40 MAD2L1 SHMT2 CSTF2 SEC24D RFC4 CCT8 PSMD11 MTCH2 MTHFD1 DUSP14 MCM7 AHSA1 HSPE1 ERGIC2 NDUFAB1 CSNK2A1 CDC7 RMI1 FASTKD3 DPAGT1 RTCB ALDOA MCTP2 NT5DC2 SLCO4A1 RANBP1 NOLC1 FEN1 EIF2S2 TMEM147 MRPL22 SUPT16H ERAL1 EIF2S1 LIMA1 COX17 CSF2 CCT7 SLC2A1 PLAGL2 PREP SEPHS1 CHAF1A RAN NT5DC3 FOCAD GABPB1 CDC20 CCNE1 SLC25A32 STRAP RAD51 PSMA3 DDX18 ENOPH1 ETNK1 up
## GSE24634_TEFF_VS_TCONV_DAY5_IN_CULTURE_UP 0.0014620 0.027915 0.4656179 2.144562 0 188 STK39 EHF MPZL1 NUP155 BRIX1 DHFR EXO1 FOXM1 TTK CENPF RBBP8 CENPM LMNB1 OLA1 CNPY2 TSFM GMNN PUS7 EAF2 TYMS RRM2 FHL2 TIPIN LRRC59 DNM1L GLO1 MELK GEMIN6 GMPS PKP4 PDCD5 UAP1 WDR12 EZH2 RAD50 ECT2 STMN1 LRPPRC IL12RB2 SKP2 ESPL1 RABIF SNRNP40 SPDL1 KIF23 PLK1 MAD2L1 SHMT2 MYBL2 RFC4 GNL3 PSMD11 KIF15 RAD1 MCM2 FAM98A MCM7 HSPE1 NDUFAB1 CDC7 HCCS UBR7 CKAP5 NABP2 KIF22 RAD54B KIF2C TRAP1 CDT1 GOT2 CHCHD3 RCC1 UBE2E3 RANBP1 ZMPSTE24 POLE3 BUB3 FEN1 CCNA1 EIF2S1 COX17 CDKN3 CCR4 PAXIP1 GPR19 KDM1A CKAP2 DSCC1 SMC4 MZB1 TRAF3IP1 NCAPD3 STIP1 KLHL7 FAF1 TUBA1C PFDN2 EIF3J PELO GGH SMC2 NFYC PABPN1 SLAMF1 DBF4 PRMT3 NUFIP1 up
## GSE27241_WT_VS_RORGT_KO_TH17_POLARIZED_CD4_TCELL_UP 0.0014948 0.027915 0.4788609 2.132162 0 142 MCM10 KNTC1 TROAP DNA2 TCERG1 FGF13 BUB1B ANLN CDCA8 TTK UBE2T MNS1 CENPF E2F8 IL24 KIF14 GMNN FANCD2 CDC6 ASPM GTSE1 MKI67 CDCA2 PRC1 AKAP12 SEC61G EZH2 TICRR ECT2 SMOC1 RACGAP1 STMN1 TPX2 KIF18B TOP2A BRCA1 UHRF1 ZRANB3 AKAP1 TTF2 KIF23 NUP205 PLK1 PIF1 AARSD1 CKAP2L KIF11 PODXL2 RPL39 POLQ KIF15 ITGA6 RAB27A STAG3 SUMO2 MEX3C HDGF CKAP5 KIF22 RAD54B XRCC2 NCAPD2 ESCO2 NEURL1B CCNF C3orf22 JUP SPAG5 C11orf24 BARD1 RBL1 LPO RFWD3 ATAD2 FUBP1 PRR11 ANAPC5 BRIP1 up
## GSE24634_TEFF_VS_TCONV_DAY3_IN_CULTURE_DN 0.0031153 0.027915 -0.4235039 -2.121422 0 186 CITED2 LTBP2 SLC31A2 MCOLN1 KLF6 OSBPL1A FIG4 RXRA RUNX1T1 MAN1C1 CAT CYP27A1 SERPING1 MARCO ABCG1 GPA33 KCTD12 HMOX1 MANBA VSIG4 RNH1 FOS FKBP15 SLC11A1 FBXW4 C1QA NCF2 GIMAP5 PILRA SLC2A9 MAN2B1 EPB41L3 RIN2 NAGLU PDCD4-AS1 DIAPH2 SPRY2 IFI30 FCGRT SAMHD1 HCK SLC7A7 KANK1 CEBPB GLB1 CYBB EVL FGR SORT1 LGALS3BP DAB2 TCEAL1 CCRL2 THEMIS2 DRAM1 down
fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='CANARY: G vs P')##
##
## pathway pval padj ES NES nMoreExtreme size leadingEdge state
## --------------------------------------------------- ---------- ---------- ----------- ---------- ------------- ----- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------
## ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER 0.0016949 0.0406155 0.6421310 2.817937 0 130 HELLS MCM10 NDC80 GINS1 KIF20A HJURP APOBEC3B DHFR STIL PAQR4 DNA2 TRIP13 FOXM1 HMMR PBK BUB1B CDCA8 TTK CENPF CDK1 E2F8 NEK2 SLC38A1 PTTG1 CCNB1 RPA3 CENPM KIF14 FANCI LMNB1 CENPA GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT CDC6 RRM2 MCM4 ASPM DSG2 GTSE1 MELK MKI67 PRC1 ASF1B NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 TPX2 PAFAH1B3 KIF18B BUB1 NETO2 TOP2A CEP55 GINS4 BRCA1 FBXO5 ESPL1 AURKB SPDL1 KIF23 PLK1 AURKA MAD2L1 MYBL2 KIFC1 KIF11 CHEK1 POLQ KIF15 MCM2 HMGA1 POLA2 MRPS15 NCAPG KIF2C CCNF SPAG5 up
## GNF2_BUB1B 0.0017301 0.0406155 0.7366708 2.753267 0 49 HELLS NDC80 GINS1 KIF20A HJURP HMMR BUB1B CDCA8 TTK CENPM KIF14 FANCI LMNB1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 PAICS MCM4 ASPM MELK ASF1B RACGAP1 BUB1 TOP2A CEP55 ESPL1 AURKB NUP205 PLK1 AURKA MCM3 KIF11 MCM2 up
## SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP 0.0016779 0.0406155 0.6183624 2.738406 0 138 LAGE3 MCM10 BLM NDC80 NME1 GINS1 KIF20A HJURP APOBEC3B MRPL15 TROAP STIL EXO1 TRIP13 FOXM1 HMMR BUB1B CDCA8 TTK CCT5 CENPF CDK1 E2F8 NEK2 PTTG1 CCNB1 PARPBP KIF14 LMNB1 CENPA CCNB2 ZWINT RRM2 MCM4 CDC25A ASPM GTSE1 MELK MKI67 GMPS PRC1 XPOT GTPBP4 NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 STMN1 TPX2 KIF18B NUDT1 BUB1 TOP2A CEP55 FBXO5 ESPL1 ORMDL2 CMC2 CDC45 AURKB POLR2K PLK1 AURKA MIS18A MAD2L1 SHMT2 MCM3 MYBL2 KIFC1 KIF11 RFC4 CHEK1 POLQ KIF15 MCM2 TIMELESS DNAJC9 HCCS RAD54B NCAPG KIF2C SPAG5 SNRPG QPRT CENPI SNRPC RNASEH2A FEN1 CDK2 CDKN3 PKMYT1 BIRC5 DSCC1 CDC20 CKS2 NCAPG2 DLGAP5 STIP1 SLC7A5 MCM6 RAD51 TIMM10 TUBA1C TXN E2F1 UBE2S ITCH CCNA2 up
## KOBAYASHI_EGFR_SIGNALING_24HR_DN 0.0015337 0.0406155 0.5613808 2.717788 0 239 TCN1 SOX9 DKK1 EREG HMGA2 TFPI2 HELLS ADORA2B MCM10 BLM NDC80 NME1 GINS1 HJURP DHFR STIL EXO1 TRIP13 HMMR PBK BUB1B POLR3K CDCA8 TTK CDK1 E2F8 NEK2 EEF1E1 TUBB2A CCNB1 DEPDC1 UCK2 CENPM KIF14 CKLF DCBLD2 FANCI LMNB1 STEAP1 CENPA GALNT10 GMNN PCNA DTL PUS7 TYMS RAD51AP1 ZWINT CDC6 RRM2 PAICS MCM4 TIPIN CDC25A ASPM GTSE1 MELK MKI67 PRC1 ASF1B GPSM2 NUSAP1 CCNE2 EZH2 ECT2 RACGAP1 CTPS1 TPX2 KIF18B MSH2 BUB1 ORC1 PRPS1 NETO2 TOP2A CEP55 IER3 BRCA1 PSAT1 SLC20A1 ESPL1 CMC2 CDC45 AURKB HSPA14 SPDL1 KIF23 PLK1 MCM5 AURKA ORC6 MAD2L1 CARD10 MCM3 MYBL2 KIF11 RFC4 DUSP5 KIF15 NOC3L FAM86C1 MCM2 ITGA6 PRIM1 POLA2 GJB3 TIMELESS MCM7 POLR2D DNAJC9 RMI1 RAD54B CKS1B MSH6 NCAPG SNRPD1 KIF2C CCNF CDT1 POLE2 SPAG5 ABCE1 SPRED2 BARD1 UNG SLCO4A1 RANBP1 UPP1 NOLC1 CDC42EP1 NT5E RNASEH2A FEN1 ZWILCH CCND1 CDK2 RFWD3 CDKN3 SPC25 RRP15 ATAD2 PLK4 ERCC6L CHAF1A PKMYT1 BIRC5 DSCC1 TUBG1 SMC4 PA2G4 CDC20 CKS2 NCAPG2 NCAPD3 DLGAP5 RRM1 MCM6 HAT1 up
## GNF2_MCM4 0.0017544 0.0406155 0.7247994 2.715373 0 52 HELLS NDC80 GINS1 FOXM1 HMMR BUB1B CDCA8 TTK CENPM KIF14 FANCI LMNB1 GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT RRM2 PAICS MCM4 ASPM MELK ASF1B RACGAP1 KIF18B BUB1 TOP2A ESPL1 AURKB MCM5 AURKA MAD2L1 MCM3 KIF11 RFC4 MCM2 MCM7 up
## GNF2_CCNA2 0.0017094 0.0406155 0.6827607 2.704433 0 65 NDC80 KIF20A HJURP FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 KIF14 FANCI CENPA GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 ASF1B NUSAP1 EZH2 RACGAP1 TPX2 KIF18B TOP2A ESPL1 AURKB PLK1 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MCM7 CKS1B NCAPG NCAPD2 up
## MODULE_54 0.0015432 0.0406155 0.5548097 2.682496 0 241 ELOVL6 PLAT ITGA2 SRPK1 KNTC1 CDCA7 DDX11 BLM NDC80 DEPDC1B TM4SF1 NME1 GINS1 HJURP APOBEC3B SNRPE DHFR TROAP TRIP13 CDK4 FOXM1 HMMR PBK BUB1B ANLN TTK UBE2T CCT5 CENPF CDK1 E2F8 CDH1 NEK2 NUF2 CCT6A PTTG1 CCNB1 RPA3 DEPDC1 RHNO1 KIF14 LMNB1 EFHC2 CENPA GMNN PCNA CCNB2 TYMS ZWINT CDC6 RRM2 MCM4 NRIP3 ASPM MELK MKI67 GAD1 ASF1B GPSM2 NUSAP1 CCNE2 MB DLEU1 ECT2 AIMP2 CTPS1 TPX2 TOPBP1 NUDT1 MSH2 BUB1 HOXC10 PSPH ORC1 BEST3 TOP2A CEP55 CDC25C LAPTM4B TMEM106C PRDX4 CDC45 AURKB AGPAT5 KIF23 PLK1 MCM5 ZNF267 AURKA MAD2L1 MCM3 MYBL2 KIFC1 KIF11 RFC4 KNSTRN CHEK1 ARL6IP1 TRIM24 MTHFD2 POLQ PHF5A MCM2 PRIM1 HMGA1 TSN TIMELESS MCM7 HSPH1 SCG5 CDC7 CDCA5 CKS1B NCAPD2 KIF2C PNP CCNF POLE2 APEX2 PMAIP1 SPAG5 NQO1 SQLE MID1 LRRC17 NT5DC2 RCC1 BARD1 UNG RANBP1 SNRPC FEN1 ZWILCH RAD54L CDKN3 ATAD2 SNRPB LRP8 CNIH4 PLK4 PRR11 AHCY CHAF1A PKMYT1 BIRC5 CKAP2 SMC4 AMPH CDC20 MUCL1 CKS2 DLGAP5 RRM1 SLC7A5 MCM6 up
## PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN 0.0022573 0.0406155 -0.7333366 -2.677611 0 38 RASL12 GRK5 ID4 MYLIP PRELP TNS1 PKIG CPED1 EMP2 MYH11 SOD3 MYLK JAM3 PTGIS LMOD1 KCNMB1 FIBIN SYNPO2 CRIM1 PKD2 ADCY9 SUSD5 ACTC1 RABGAP1 HSPB1 down
## WONG_ENDMETRIUM_CANCER_DN 0.0024096 0.0406155 -0.6220488 -2.641399 0 76 LTBP4 TBX3 MASP1 GAS6 DPP6 EDNRB WNT4 LDB2 JPH4 RUNX1T1 HIC1 SFRP4 LMOD1 KIF26A F10 MME TSHZ3 CTSW SYNPO2 PID1 PDGFRA COX7A1 PEG3 EHD2 XYLT1 EFS SLC24A3 CNRIP1 GNLY MICU3 VGLL3 EMILIN1 TWIST2 SLC18A2 TCEAL7 ADAMTS5 down
## GNF2_RRM2 0.0018018 0.0406155 0.7454536 2.637705 0 39 NDC80 FOXM1 HMMR BUB1B CDCA8 CENPF CDK1 CENPM LMNB1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 NUSAP1 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA MCM3 KIF11 MCM2 up
## VANHARANTA_UTERINE_FIBROID_DN 0.0024038 0.0406155 -0.6447834 -2.621498 0 61 CITED2 NR3C1 SMAD7 EGR1 GIMAP6 KLF4 IER2 CBX7 PHYHIP ODC1 HOXA5 GATA2 KLF2 APOL3 WFS1 SOX17 GSTM5 ATF3 RARRES2 LTBP1 PTCH1 NR4A2 DAPK1 MAFF ABCA8 ADH1B PTGER3 TFPI TRIB1 LEPR ACKR3 C1R down
## GNF2_PCNA 0.0017094 0.0406155 0.6584105 2.607981 0 65 NDC80 GINS1 FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 TPX2 KIF18B MSH2 TOP2A ESPL1 MCM5 AURKA MCM3 MYBL2 KIF11 RFC4 KIF15 MCM2 PRIM1 MCM7 DNAJC9 POLE2 FEN1 RAD54L PAXIP1 PLK4 BIRC5 SMC4 PA2G4 CDC20 CKS2 DLGAP5 RRM1 MCM6 HNRNPAB up
## VECCHI_GASTRIC_CANCER_EARLY_UP 0.0014388 0.0406155 0.5070409 2.585527 0 403 ATP10B SLC4A11 MYEOV TMEM45B ILDR1 NUP62CL CLDN2 GUCY2C KCNN4 E2F7 TMC5 CLDN1 LACTB2 LCN2 HOXA10 CENPH ITGA2 CENPK ADORA2B ZNF117 MCM10 TMPRSS4 CDCA7 PMS2P5 FERMT1 STRIP2 NDC80 PDP1 MUC13 DEPDC1B TM4SF1 C12orf66 NME1 CDH17 GINS1 MMP7 KIF20A NUP155 DHFR FIGNL1 PDCD6 TRIP13 EFNA4 FOXM1 HMMR PBK BUB1B ANLN PI3 TTK SATB2-AS1 UBE2T CENPF CDK1 E2F8 MACC1 NEK2 NUF2 XPO5 RP9 CLRN3 PTTG1 CCT3 CCNB1 RPA3 DEPDC1 PARPBP TRMT6 CENPM KIF14 FANCI ZIC2 CENPA SEMA4B DTL PUS7 LAMC2 MARVELD3 CCNB2 STK31 RAD51AP1 ZWINT FANCD2 CDC6 RRM2 MCM4 UCHL3 NUDCD1 ASPM S100A11 LIF SFXN4 GTSE1 MELK OVOL1 MKI67 KLK6 PABPC1L CDCA2 PRC1 GTPBP4 HOXA9 GAD1 GPSM2 NUSAP1 PROX1 MSX2 EZH2 TFAP2C ECT2 RACGAP1 S100A6 TPX2 KIF18B TFAP2A CXCL1 KRT18 BUB1 TIMM17A TOP2A CEP55 GINS4 BRCA1 LAPTM4B UHRF1 SKP2 NPM1 TRIM31 HOXC6 EIF3B ENO1 SPDL1 MCM5 AURKA MAD2L1 MYBL2 RAD18 PITPNB CHEK1 SKA3 CEP72 THOC3 KIF15 MCM2 SLC39A10 MYOF MTCH2 NEAT1 HMGA1 WDR72 CENPW PGRMC1 ITPA ARL5B MCM7 HSPE1 DCAF13 HSPH1 XRCC4 POLD3 CDCA5 RAD54B CKS1B HUS1 NCAPG SNRPD1 ESCO2 APEX2 JUP CDH3 EML4 MRPL13 ABHD10 ZNF367 BARD1 RANBP1 UPP1 BUB3 STK3 FEN1 WDR90 KCNE3 ATG16L1 CHI3L1 CDKN3 NMU ATAD2 FUBP1 SNRPB LRP8 PRR11 DPP3 SPP1 S100A10 BRIP1 PMEPA1 BIRC5 CKAP2 DSCC1 RRS1 SMC4 ZDHHC11 MRPS10 PTMAP4 CDK12 CDC20 CKS2 NCAPG2 CCNE1 CSTF3 FAM50A DLGAP5 PDZK1IP1 up
## chr12q15 0.0017825 0.0406155 0.7543284 2.583216 0 34 FAHD2P1 RN7SL804P CPSF6 IL26 CCT2 YEATS4 NUP107 MYRFL MDM1 RAB3IP PRELID2P1 IL22 KRT8P39 IFNG-AS1 MRPL40P1 MDM2 FRS2 CNOT2 HNRNPA1P70 SLC35E3 PTPRR RAP1B SNORA70G BEST3 IFNG DYRK2 RPL39P28 up
## GNF2_RRM1 0.0017036 0.0406155 0.6221144 2.571186 0 86 NDC80 GINS1 DHFR FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 CCT6A CENPM KIF14 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT RRM2 PAICS MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 KIF18B MSH2 TOP2A AURKB MCM5 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MRPL35 MCM7 SNRPD1 CHCHD3 SNRPG FEN1 EIF2S1 PLK4 PCCB RAN BIRC5 SMC4 PA2G4 CDC20 CKS2 DLGAP5 RRM1 MCM6 FH HAT1 HNRNPAB SERBP1 ANP32E SMC2 CCNA2 up
## GNF2_HMMR 0.0017301 0.0406155 0.6926553 2.560950 0 46 NDC80 KIF20A FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 E2F8 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA KIF11 MCM2 up
## GSE15750_DAY6_VS_DAY10_EFF_CD8_TCELL_UP 0.0016502 0.0406155 0.5465044 2.541129 0 181 E2F7 SPAG1 CENPH HELLS MCM10 KNTC1 MUC20 NDC80 GINS1 KIF20A DHFR FIGNL1 STIL DNA2 HMMR PBK BUB1B CDCA8 TTK CDK1 NEK2 RBBP8 NUF2 RPA3 DEPDC1 PARPBP CENPM PMCH CENPA GMNN PSMG4 IQGAP3 CCNB2 RAD51AP1 CDC6 RRM2 FHL2 TIPIN PTPRK ASPM PSMD1 GTSE1 MELK C1orf112 RAD51B PRC1 LSM12 ASF1B NUSAP1 C12orf75 RACGAP1 STMN1 TPX2 KIF18B TCF19 BUB1 TOP2A CEP55 BRCA1 CDC25C UHRF1 FBXO5 ESPL1 PRDX4 MRPL9 CDC45 AURKB SPDL1 PASK KIF23 PLK1 MCM5 AURKA MAD2L1 MYBL2 CKAP2L KIF11 KNSTRN SKA3 PPIL1 POLQ MCM2 CENPW MCM7 ALDH7A1 KIF22 RAD54B CKS1B NCAPG CASP3 ESCO2 NEURL1B KIF2C TAX1BP3 SPAG5 up
## WHITEFORD_PEDIATRIC_CANCER_MARKERS 0.0017271 0.0406155 0.5903122 2.533225 0 108 MND1 CDCA7 NME1 DHFR CDK4 PBK CDCA8 TTK UBE2T CENPF CDK1 NEK2 NUF2 PTTG1 CCNB1 KIF14 CENPA ILF2 PCNA PON3 CCNB2 TYMS ZWINT RRM2 MCM4 CDC25A MELK MKI67 CDCA2 PRC1 GAPDH ASF1B NUSAP1 GPX7 STMN1 TPX2 PAFAH1B3 NUDT1 BUB1 TOP2A PSAT1 SOX4 UHRF1 ESPL1 CCDC34 CDC45 ENO1 MCM5 AURKA RCC2 MAD2L1 MYBL2 KIF11 RFC4 POLQ up
## WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP 0.0016750 0.0406155 0.5734851 2.529057 0 134 UNC5CL CD24 STK39 ELOVL6 GDA TOX3 TSPAN8 GALNT3 BZW2 KDELR2 PLS1 FRK LRRC8B SYT13 PERP GMDS OCIAD2 BRI3BP GALNT7 NET1 SYTL2 GFPT1 SFXN1 RASSF6 ABCC3 EPCAM KCNK1 CPD NME7 EDEM3 TPD52 GALNT4 GOLPH3 PDZD8 C3orf52 ESRP1 GNPNAT1 SEC24A COX7A2 ECT2 ASPHD2 MYO6 RASEF CASK GPR160 CHMP4C ABHD17C SH3RF1 ERBB3 SFN MAL2 DDAH1 ITGA6 ATP8B1 ELL3 TMEM30B ATP1B1 TSTA3 SLC35A3 ABCD3 SAR1B ARHGAP12 TMED4 PBLD NQO1 MAP7 MUC1 TNPO1 CTSE ARSD LLGL2 FNIP2 CA2 GPATCH4 ABHD2 ACBD5 TM9SF3 up
## GNF2_SMC4L1 0.0016835 0.0406155 0.6129553 2.525218 0 80 NDC80 GINS1 DHFR FOXM1 HMMR BUB1B CDCA8 TTK CBX3 CENPF CDK1 E2F8 FANCI GMNN PCNA DTL CCNB2 TYMS RAD51AP1 ZWINT MCM4 ASPM PRC1 NUSAP1 SRSF1 RACGAP1 KIF18B MSH2 TOP2A FBXO5 MCM5 AURKA MCM3 KIF11 RFC4 MCM2 PRIM1 MRPL35 MCM7 DNAJC9 SNRPD1 POLE2 SNRPG FEN1 ZWILCH SUPT16H EIF2S1 GAR1 PLK4 PCCB CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 HAT1 HNRNPAB SERBP1 ANP32E SMC2 CCNA2 up
## GNF2_CDC2 0.0017123 0.0406155 0.6533356 2.517694 0 59 NDC80 KIF20A HJURP FOXM1 HMMR CDCA8 TTK CENPF CDK1 E2F8 PTTG1 FANCI PCNA CCNB2 TYMS ZWINT RRM2 ASPM MELK MKI67 PRC1 NUSAP1 EZH2 TPX2 KIF18B TOP2A AURKA MYBL2 KIFC1 KIF11 RFC4 KIF15 MCM2 PRIM1 DNAJC9 NCAPG CCNF FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 up
## GNF2_RFC4 0.0017606 0.0406155 0.6598827 2.510264 0 57 CCT2 MCM10 KNTC1 NDC80 GINS1 SNRPE FOXM1 TTK CENPF CDK1 RPA3 FANCI GMNN PCNA CCNB2 TYMS RAD51AP1 ZWINT PAICS MCM4 ASPM CTPS1 MSH2 TOP2A MCM3 KIF11 RFC4 MCM2 PRIM1 TIMELESS MCM7 CKS1B MSH6 NCAPD2 SNRPD1 RANBP1 FEN1 SUPT16H RAD54L PLK4 RAN BIRC5 SMC4 CKS2 RRM1 MCM6 up
## ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 0.0016667 0.0406155 0.5482005 2.508475 0 166 LEMD1 STYK1 SLC4A11 MYEOV CKMT1B KCNN4 DKK1 C1GALT1 RHBDL2 GPR87 SCIN PPP1R1B GCNT3 OLFM4 ITGA2 CEACAM5 FA2H GJB4 GALNT6 SOX21 TMPRSS4 TUFT1 FERMT1 BCL2L15 CDH17 SLC6A20 ANKRD22 VSTM2L SIX4 QPCT AP1S3 GPR35 REG4 BIK ANLN LGALS4 TTK KCNK1 CYP2S1 LAMC2 SERPINB5 CCNB2 CDX2 PTPRR C15orf48 KLK6 MYO1A APOBEC1 TPX2 ASPHD2 DTX2 BUB1 TOP2A CEP55 GPR160 HSH2D TRIM31 MUC17 KRT19 PPP1R14D AURKA TJP3 KIF11 TSPAN1 NFE2L3 KIF15 SFN GJB5 MYOM3 ELL3 GJB3 LIPH DAPP1 ST14 SERPINB2 CST6 LGALS3 PMAIP1 CDH3 CBLC LAMB3 TFCP2L1 IGFL2 CTSE KRT6B up
## GNF2_PA2G4 0.0016835 0.0406155 0.6151580 2.506445 0 75 LSM5 CCT2 NUP107 NDC80 MRPL15 SNRPE XRCC5 CDK4 BUB1B CCT5 CCT6A CCT3 CENPM OLA1 GMNN PCNA PAICS MCM4 MRPL3 MELK ETFA GMPS SSBP1 CCT4 LRPPRC MCM5 MCM3 NAE1 MTHFD2 PSMD11 METTL5 MRPL35 MCM7 CKS1B SNRPA SNRPD1 ABCE1 CHCHD3 SNRPG RANBP1 BUB3 MRPL22 EIF2S1 SNRPB CAD RAN PSMA4 PA2G4 RRM1 FH HAT1 NDUFS1 NCL PSMA3 HNRNPA2B1 SERBP1 CSE1L up
## NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON 0.0017730 0.0406155 0.6951402 2.505845 0 42 TSPAN8 CPSF6 IL26 METTL1 CCT2 YEATS4 NUP107 MDM1 C12orf66 RAB3IP IL22 CDK4 AVIL CAND1 MDM2 FRS2 CNOT2 TSFM C12orf56 SLC35E3 PTPRR RAP1B XPOT TSPAN31 BEST3 LGR5 IFNG DYRK2 TBK1 CTDSP2 ZFC3H1 CYP27B1 OS9 up
## CROONQUIST_IL6_DEPRIVATION_DN 0.0017271 0.0406155 0.6005625 2.493056 0 91 KNTC1 GINS1 APOBEC3B DHFR STIL TRIP13 FOXM1 HMMR BUB1B CDK1 PTTG1 CCNB1 KIF14 FANCI CENPA PCNA CCNB2 TYMS ZWINT CDC6 RRM2 MCM4 CDC25A MKI67 GMPS CCNE2 STMN1 TPX2 FRZB BUB1 TOP2A BRCA1 SKP2 GALE CDC45 AURKB PLK1 AURKA MAD2L1 MCM3 MYBL2 KIFC1 KIF11 CHEK1 MCM2 HMGA1 MCM7 KIF22 CKS1B KIF2C TRAIP CCNF POLE2 SPAG5 PTP4A3 CDKN3 SPC25 PLK4 SEPHS1 SPP1 CHAF1A SMC4 CDC20 CKS2 up
## GSE21063_WT_VS_NFATC1_KO_8H_ANTI_IGM_STIM_BCELL_UP 0.0016556 0.0406155 0.5387389 2.489696 0 178 ELOVL6 E2F7 KCNK5 LACTB2 YEATS4 MCM10 CDCA7 GPT2 NDC80 BDH1 DEPDC1B GMDS SLC27A2 INPP4B HJURP DHFR CHEK2 EXO1 TCEA1 BUB1B ANLN TTK UBE2T CDK1 SFXN1 E2F8 MNAT1 RBBP8 NUF2 CCNB1 PARPBP UCK2 CENPL MBOAT1 DTL TYMS TSPAN5 AP2B1 CDC6 TIPIN CDC25A ASPM MELK MKI67 CDCA2 PRC1 XPOT WDR12 ASF1B CCNE2 DLEU1 EZH2 ECT2 TPX2 KIF18B BUB1 TOP2A WDYHV1 PSAT1 TMEM106C FBXO5 VANGL1 AURKB MCM5 PIF1 AURKA ORC6 MAD2L1 SUV39H2 KIFC1 KIF11 RFC4 SRI IFI27L1 CHEK1 RHEBL1 KIF15 PRIM1 LRRC20 MTHFD1 PRPS2 ALG8 POLA2 up
## GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_UP 0.0016367 0.0406155 0.5340132 2.489455 0 188 MND1 E2F7 KIF2A CENPH ITGA2 CENPK CCT2 MCM10 MUC20 KIF20A DHFR STIL DNA2 EXO1 FOXM1 HMMR PBK BUB1B ANLN TTK CENPF CDK1 E2F8 NEK2 NUF2 DEPDC1 PARPBP CENPM PMCH CENPA PCNA DTL CCNB2 RAD51AP1 FANCD2 CDC6 RRM2 GEN1 ASPM CDCA7L FAM221A RBMX CLSPN GTSE1 MELK MKI67 CDCA2 TICRR ECT2 RACGAP1 STMN1 TPX2 KIF18B TCF19 BUB1 ORC1 TOP2A CEP55 PSAT1 CDC25C UHRF1 CDC45 AURKB SPDL1 PASK KIF23 NUP205 PLK1 PIF1 AURKA CCAR1 MAD2L1 MCM3 MYBL2 CKAP2L KNSTRN CHEK1 SKA3 SYNRG EME1 PRIM1 CPOX CKAP5 KIF22 CDCA5 CKS1B NCAPG ESCO2 FAM114A1 CCNF SPAG5 SQLE NMRAL1 CENPI FEN1 PRSS16 ZWILCH KIF20B SPC24 CDKN3 SPC25 CCDC43 PRR11 BRIP1 AUNIP CENPP BIRC5 CTLA4 CKAP2 up
## GNF2_CENPF 0.0017182 0.0406155 0.6476011 2.486228 0 58 MCM10 NDC80 HJURP FOXM1 HMMR CDCA8 TTK CENPF CDK1 E2F8 PTTG1 FANCI PCNA CCNB2 TYMS ZWINT RRM2 ASPM MKI67 PRC1 NUSAP1 TPX2 KIF18B TOP2A AURKA MCM3 MYBL2 KIFC1 KIF11 RFC4 KIF15 MCM2 PRIM1 MCM7 DNAJC9 CCNF FEN1 PLK4 BIRC5 CKAP2 SMC4 CDC20 CKS2 DLGAP5 RRM1 HAT1 up
## GNF2_CDC20 0.0017606 0.0406155 0.6604844 2.485176 0 53 NDC80 KIF20A FOXM1 HMMR BUB1B CDCA8 TTK CENPF CDK1 PTTG1 GMNN PCNA CCNB2 TYMS ZWINT RRM2 MCM4 ASPM MELK MKI67 PRC1 NUSAP1 RACGAP1 TPX2 KIF18B BUB1 TOP2A ESPL1 AURKB PLK1 AURKA KIF11 MCM2 CKS1B KIF2C SPAG5 PLK4 RAN BIRC5 SMC4 CDC20 CKS2 DLGAP5 RRM1 up